Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix

--- a/abundance_estimates_to_matrix.xml	Mon Jan 22 11:28:19 2018 -0500
+++ b/abundance_estimates_to_matrix.xml	Thu Jun 14 03:12:12 2018 -0400
@@ -1,12 +1,12 @@
-<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.2">
+<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@">
     <description>for a de novo assembly of RNA-Seq data by Trinity</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.20.1">bioconductor-edger</requirement>
+        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
         <requirement type="package" version="0.9.1">salmon</requirement>
-        <requirement type="package" version="0.43.1">kallisto</requirement>
+        <requirement type="package" version="0.44.0">kallisto</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
         #import re
@@ -19,13 +19,38 @@
         --est_method ${est_method}
         --cross_sample_norm ${additional_params.cross_sample_norm}

+        #if $gene_trans_map:
+            --gene_trans_map '$gene_trans_map'
+        #else:
+            --gene_trans_map 'none'
+        #end if
+
         #for $entry in $samples:
             '${re.sub('[^\w\-_]', '_', entry.element_identifier)}'
         #end for
+
+        && mv *.isoform.counts.matrix '$trans_counts'
+        && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm'
+        #if $gene_trans_map:
+            && mv *.gene.counts.matrix '$trans_counts_gene'
+            && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene'
+        #end if
+
+        #if $additional_params.cross_sample_norm == "TMM":
+            && mv *.isoform.TMM.EXPR.matrix '$norm_TMM'
+            #if $gene_trans_map:
+                && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene'
+            #end if
+        #else if $additional_params.cross_sample_norm == "UpperQuartile":
+            && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ'
+            #if $gene_trans_map:
+                && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene'
+            #end if
+        #end if
     ]]></command>
     <inputs>
         <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
-
+        <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" />
         <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
             <option value="RSEM">RSEM</option>
             <option value="eXpress">eXpress</option>
@@ -42,14 +67,29 @@
         </section>
     </inputs>
     <outputs>
-        <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/>
-        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/>
-        <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix">
+        <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/>
+        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/>
+
+        <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)">
+            <filter>gene_trans_map</filter>
+        </data>
+        <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)">
+            <filter>gene_trans_map</filter>
+        </data>
+
+        <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
         </data>
-        <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix">
+        <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
         </data>
+
+        <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
+            <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter>
+        </data>
+        <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
+            <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -68,7 +108,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />
@@ -91,7 +131,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />
@@ -114,7 +154,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />
@@ -137,7 +177,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_UQ">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                 </assert_contents>
@@ -193,7 +233,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />
--- a/macros.xml	Mon Jan 22 11:28:19 2018 -0500
+++ b/macros.xml	Thu Jun 14 03:12:12 2018 -0400
@@ -2,19 +2,19 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.4.0">trinity</requirement>
+            <requirement type="package" version="2.6.6">trinity</requirement>
             <yield/>
         </requirements>
     </xml>

-    <token name="@WRAPPER_VERSION@">2.4.0</token>
+    <token name="@WRAPPER_VERSION@">2.6.6</token>

     <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
-        #if $inputs.strand.is_strand_specific:
-            --SS_lib_type $inputs.strand.library_type
+        #if $pool.inputs.strand.is_strand_specific:
+            --SS_lib_type $pool.inputs.strand.library_type
         #end if

-        $inputs.jaccard_clip
+        $pool.inputs.jaccard_clip
     </token>

     <xml name="input_paired_strand_jaccard">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/Trinity.map	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,7 @@
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
--- a/test-data/count/analyze_diff_expr/results.matrix	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/analyze_diff_expr/results.matrix	Thu Jun 14 03:12:12 2018 -0400
@@ -1,14 +1,14 @@
-	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR3788|c0_g1_i1	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
 TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
-TR4277|c0_g1_i1	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR3091|c0_g1_i1	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
 TR2779|c0_g1_i1	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
-TR2672|c0_g1_i1	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
-TR127|c1_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
 TR2107|c1_g1_i1	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR4761|c0_g1_i1	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
 TR5055|c0_g2_i1	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
-TR3091|c0_g1_i1	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
-TR4761|c0_g1_i1	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR5075|c0_g1_i1	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
+TR2672|c0_g1_i1	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR4277|c0_g1_i1	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR127|c1_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
 TR131|c0_g1_i1	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
-TR5075|c0_g1_i1	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
 TR1894|c2_g1_i1	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
-TR3788|c0_g1_i1	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
Binary file test-data/count/analyze_diff_expr/results.matrix.RData has changed
--- a/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat	Thu Jun 14 03:12:12 2018 -0400
@@ -1,14 +1,14 @@
 wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR3788|c0_g1_i1	-1.22775484082629	-0.443483531881724	-0.874117886211586	1.12588211378841	1.65760259323259	1.57960008123132	-0.353285722910146	-0.874117886211586	-0.590324920210995
 TR24|c0_g1_i1	0.106533882165825	-0.313797916782532	0.025003996669227	-1.19180739240392	-1.23133575659056	-1.2719777410879	1.39963914188743	1.22079106142351	1.25695072471892
-TR4277|c0_g1_i1	3.24415794782388	3.31812623217364	3.18414689752048	-1.98611482817144	-1.80411699442855	-1.51461037723356	-1.44630436384266	-1.5322044372483	-1.46308007659348
+TR3091|c0_g1_i1	-2.42438780178849	-2.77802475640319	-2.62602166295814	1.02359379610527	1.32351327005887	1.20686835120661	1.43575453462855	1.4783149968566	1.36038927229391
 TR2779|c0_g1_i1	-0.795433018475884	-1.23380302158535	-0.574143153586594	-1.13287411273457	-0.795433018475884	-0.712970858283911	1.74646076035339	1.75438767612502	1.74380874666379
-TR2672|c0_g1_i1	0.965440325233136	1.96544032523314	1.58211168568163	-2.94145027037538	-0.619522175488021	-1.35648776965423	0.965440325233136	-0.619522175488021	0.0585497296246169
-TR127|c1_g1_i1	1.25755965737847	2.52059406321227	2.02309440374145	-0.479405936787734	-2.06436843750889	-1.06436843750889	-0.0643684375088904	-1.06436843750889	-1.06436843750889
 TR2107|c1_g1_i1	2.49178842221691	2.62929194596684	2.16986032732955	-0.607747251334006	-0.607747251334006	-0.41510217339161	-1.41510217339161	-2.41510217339161	-1.83013967267045
+TR4761|c0_g1_i1	2.06406810079911	1.80544476674762	1.90822498634624	-1.67981690730689	-1.51400801433681	-1.59017969482221	-0.339510283104669	-0.357888812419525	-0.296334141902888
 TR5055|c0_g2_i1	1.90528891290538	0.865760548718745	1.50319046933404	-0.982236357836205	-0.304164452723568	-1.30416445272357	-0.982236357836205	-0.982236357836205	0.280798047997588
-TR3091|c0_g1_i1	-2.42438780178849	-2.77802475640319	-2.62602166295814	1.02359379610527	1.32351327005887	1.20686835120661	1.43575453462855	1.4783149968566	1.36038927229391
-TR4761|c0_g1_i1	2.06406810079911	1.80544476674762	1.90822498634624	-1.67981690730689	-1.51400801433681	-1.59017969482221	-0.339510283104669	-0.357888812419525	-0.296334141902888
+TR5075|c0_g1_i1	-1.04544737992556	-0.329240345926152	-0.393370683345868	-2.04544737992556	-1.68287730054085	-1.39337068334587	2.50474970263492	2.07793503557972	2.30706903479522
+TR2672|c0_g1_i1	0.965440325233136	1.96544032523314	1.58211168568163	-2.94145027037538	-0.619522175488021	-1.35648776965423	0.965440325233136	-0.619522175488021	0.0585497296246169
+TR4277|c0_g1_i1	3.24415794782388	3.31812623217364	3.18414689752048	-1.98611482817144	-1.80411699442855	-1.51461037723356	-1.44630436384266	-1.5322044372483	-1.46308007659348
+TR127|c1_g1_i1	1.25755965737847	2.52059406321227	2.02309440374145	-0.479405936787734	-2.06436843750889	-1.06436843750889	-0.0643684375088904	-1.06436843750889	-1.06436843750889
 TR131|c0_g1_i1	-3.50802026981862	-3.6944333940495	-3.55241438917708	1.41625240401813	1.71671228997234	1.68718414007205	1.98577454287534	1.99158406095747	1.95736061514986
-TR5075|c0_g1_i1	-1.04544737992556	-0.329240345926152	-0.393370683345868	-2.04544737992556	-1.68287730054085	-1.39337068334587	2.50474970263492	2.07793503557972	2.30706903479522
 TR1894|c2_g1_i1	2.11263053903627	1.56008951600749	1.23816142112012	-1.34680107960103	-0.761838578879876	0.238161421120124	-1.34680107960103	-0.346801079601032	-1.34680107960103
-TR3788|c0_g1_i1	-1.22775484082629	-0.443483531881724	-0.874117886211586	1.12588211378841	1.65760259323259	1.57960008123132	-0.353285722910146	-0.874117886211586	-0.590324920210995
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf has changed
--- a/test-data/count/analyze_diff_expr/results.matrix.log2.dat	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat	Thu Jun 14 03:12:12 2018 -0400
@@ -1,14 +0,0 @@
-wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
-TR24|c0_g1_i1	6.5077946401987	6.08746284125034	6.4262647547021	5.20945336562895	5.16992500144231	5.12928301694497	7.8008998999203	7.62205181945638	7.65821148275179
-TR4277|c0_g1_i1	12.1250905393033	12.199058823653	12.0650794889999	6.89481776330794	7.07681559705083	7.36632221424582	7.43462822763672	7.34872815423108	7.4178525148859
-TR2779|c0_g1_i1	7.54689445988764	7.10852445677817	7.76818432477693	7.20945336562895	7.54689445988764	7.62935662007961	10.0887882387169	10.0967151544885	10.0861362250273
-TR2672|c0_g1_i1	3.90689059560852	4.90689059560852	4.52356195605701	0	2.32192809488736	1.58496250072116	3.90689059560852	2.32192809488736	3
-TR127|c1_g1_i1	3.32192809488736	4.58496250072116	4.08746284125034	1.58496250072116	0	1	2	1	1
-TR2107|c1_g1_i1	5.90689059560852	6.04439411935845	5.58496250072116	2.8073549220576	2.8073549220576	3	2	1	1.58496250072116
-TR5055|c0_g2_i1	5.20945336562895	4.16992500144231	4.8073549220576	2.32192809488736	3	2	2.32192809488736	2.32192809488736	3.58496250072116
-TR3091|c0_g1_i1	4.52356195605701	4.16992500144231	4.32192809488736	7.97154355395077	8.27146302790437	8.1548181090521	8.38370429247405	8.4262647547021	8.30833903013941
-TR4761|c0_g1_i1	11.0292872269682	10.7706638929168	10.8734441125154	7.28540221886225	7.45121111183233	7.37503943134692	8.62570884306447	8.60733031374961	8.66888498426625
-TR131|c0_g1_i1	5.04439411935845	4.85798099512757	5	9.96866679319521	10.2691266791494	10.2395985292491	10.5381889320524	10.5439984501345	10.5097750043269
-TR5075|c0_g1_i1	3.8073549220576	4.52356195605701	4.4594316186373	2.8073549220576	3.16992500144231	3.4594316186373	7.35755200461808	6.93073733756289	7.15987133677839
-TR1894|c2_g1_i1	4.4594316186373	3.90689059560852	3.58496250072116	1	1.58496250072116	2.58496250072116	1	2	1
-TR3788|c0_g1_i1	4.16992500144231	4.95419631038687	4.52356195605701	6.52356195605701	7.05528243550119	6.97727992349992	5.04439411935845	4.52356195605701	4.8073549220576
--- a/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat	Thu Jun 14 03:12:12 2018 -0400
@@ -1,10 +0,0 @@
-wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
-wt_37_2	1	0.968650822800566	0.985499030254524	0.457364683078012	0.443497697874748	0.451451348748615	0.41961787977306	0.444203836374748	0.448348619980356
-wt_37_3	0.968650822800566	1	0.98879028662025	0.400031307625771	0.378330685571456	0.396636302989378	0.39057945325073	0.383299487197462	0.388022080096891
-wt_37_1	0.985499030254524	0.98879028662025	1	0.452638132682111	0.434834315692609	0.44176483058741	0.461437515072935	0.462172448553839	0.473652431554024
-wt_GSNO_3	0.457364683078012	0.400031307625771	0.452638132682111	1	0.965144031362199	0.979742518682039	0.844139129634192	0.862862111399854	0.857171072391268
-wt_GSNO_1	0.443497697874748	0.378330685571456	0.434834315692609	0.965144031362199	1	0.983818328020852	0.858668155107621	0.871693931267863	0.876908826664397
-wt_GSNO_2	0.451451348748615	0.396636302989378	0.44176483058741	0.979742518682039	0.983818328020852	1	0.854388461031158	0.878292745544781	0.861156659158544
-wt_ph8_3	0.41961787977306	0.39057945325073	0.461437515072935	0.844139129634192	0.858668155107621	0.854388461031158	1	0.984071267766826	0.98764423106737
-wt_ph8_1	0.444203836374748	0.383299487197462	0.462172448553839	0.862862111399854	0.871693931267863	0.878292745544781	0.984071267766826	1	0.989191009161984
-wt_ph8_2	0.448348619980356	0.388022080096891	0.473652431554024	0.857171072391268	0.876908826664397	0.861156659158544	0.98764423106737	0.989191009161984	1
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf has changed
--- a/test-data/count/contig_exn50_statistic/ExN50.stats	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/contig_exn50_statistic/ExN50.stats	Thu Jun 14 03:12:12 2018 -0400
@@ -1,5 +1,4 @@
-#E	min_expr	E-N50	num_transcripts
-E33	525311.050	541	1
-E67	525311.050	541	2
-E99	329523.810	380	3
-E100	0	279	7
+Ex	ExN50	num_transcripts
+33	541	1
+67	541	2
+100	279	7
Binary file test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,38 +1,38 @@
 sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
-TR4277|c0_g1_i1	wt_37	wt_GSNO	3852.97388871986	161.116814813422	2007.04535176664	4.57260002898197	0.121471586836965	37.6433711623376	0	0
-TR131|c0_g1_i1	wt_37	wt_GSNO	26.1866396538608	1340.30918254958	683.247911101723	-5.67373033438939	0.187375754459626	-30.2799599166492	2.10486694333775e-201	3.89400384517483e-200
-TR4761|c0_g1_i1	wt_37	wt_GSNO	1645.20640957447	193.196157329029	919.201283451752	3.08848040390227	0.143569117275296	21.5121501233448	1.19819880470067e-102	1.47777852579749e-101
-TR3091|c0_g1_i1	wt_37	wt_GSNO	16.7444693227929	328.569936894811	172.657203108802	-4.29037251456992	0.240582794801874	-17.8332474610379	3.90090325510546e-71	3.60833551097255e-70
-TR3638|c0_g1_i1	wt_37	wt_GSNO	583.00358519031	183.754416330029	383.37900076017	1.66018954854466	0.144513974558734	11.4880900176883	1.51422805973163e-30	1.12052876420141e-29
-TR2487|c0_g1_i1	wt_37	wt_GSNO	342.210853400436	920.407318992504	631.30908619647	-1.42691086642688	0.124648977132644	-11.4474334186348	2.42211055832184e-30	1.49363484429847e-29
-TR3788|c0_g1_i1	wt_37	wt_GSNO	19.5075441237117	134.95369713876	77.2306206312357	-2.77036684869735	0.263152237265066	-10.527620351967	6.4442989603998e-26	3.40627230763989e-25
-TR1479|c0_g1_i1	wt_37	wt_GSNO	129.593534475689	371.064629188207	250.329081831948	-1.51441062491813	0.145530800926874	-10.4061175728641	2.32511621828936e-25	1.07536625095883e-24
-TR2107|c1_g1_i1	wt_37	wt_GSNO	48.9228907410258	7.40521775805688	28.1640542495414	2.69488884014666	0.432209832999676	6.23514005094067	4.51374085119887e-10	1.85564901660398e-09
-TR3854|c0_g1_i1	wt_37	wt_GSNO	1573.69549271337	2374.56159860719	1974.12854566028	-0.593515573382884	0.111170659243154	-5.33877893163104	9.35746583039244e-08	3.4622623572452e-07
-TR2122|c0_g2_i2	wt_37	wt_GSNO	119.534640490118	199.143666337033	159.339153413576	-0.738644008220832	0.168659021315898	-4.37951081690053	1.18946017688789e-05	4.00091150407745e-05
-TR1449|c0_g1_i1	wt_37	wt_GSNO	180.814952011467	104.755290736358	142.785121373912	0.784193680180578	0.186004942516637	4.21598302480827	2.48692468039376e-05	7.49709472786912e-05
-TR4163|c0_g1_i1	wt_37	wt_GSNO	347.283468916919	232.772947466212	290.028208191566	0.576743600823335	0.13722219355458	4.20299068163444	2.63411436384591e-05	7.49709472786912e-05
-TR2672|c0_g1_i1	wt_37	wt_GSNO	18.3155337236093	2.26581902751323	10.2906763755613	2.88788179640237	0.725539563189254	3.98032298019437	6.88216980025882e-05	0.000181885916149697
-TR127|c1_g1_i1	wt_37	wt_GSNO	13.461799216177	1.21881296083961	7.34030608850831	3.33150202228086	0.915899815581865	3.63740877070095	0.000275394687501815	0.000667511143840185
-TR5055|c0_g2_i1	wt_37	wt_GSNO	23.3590211688541	5.52768338415684	14.4433522765055	2.04460941512382	0.563987307210913	3.62527558507482	0.000288653467606567	0.000667511143840185
-TR2844|c0_g1_i1	wt_37	wt_GSNO	158.206282615139	231.762548186068	194.984415400603	-0.550639207704626	0.154913717539885	-3.55448966333699	0.000378713397971402	0.000824258572055403
-TR5212|c0_g1_i1	wt_37	wt_GSNO	65.7079302129484	107.875371765755	86.7916509893515	-0.713874873222434	0.210087143945163	-3.39799408862815	0.000678818868686303	0.00139534989674407
-TR1894|c2_g1_i1	wt_37	wt_GSNO	13.3497721959996	2.96749216411516	8.15863218005739	2.04972102673103	0.716146945354672	2.86215146210796	0.00420775772107294	0.00819405450945783
-TR24|c0_g1_i1	wt_37	wt_GSNO	69.9065207344592	41.2394742844514	55.5729975094553	0.760351613917761	0.269735390145923	2.81887969356346	0.00481915767774413	0.00891544170382664
-TR2779|c0_g1_i1	wt_37	wt_GSNO	155.915506826481	205.619872596257	180.767689711369	-0.402350189521528	0.18910416680051	-2.12766432558821	0.0333649247395808	0.0587858197792614
-TR3807|c0_g1_i1	wt_37	wt_GSNO	3.48709246029019	0.350050334268211	1.9185713972792	2.6523001983829	1.38324824664578	1.91744338358239	0.055181627150862	0.092164962039527
-TR1492|c0_g1_i2	wt_37	wt_GSNO	1640.89375005483	1435.64893261411	1538.27134133447	0.192484568368337	0.101250195527162	1.90107848548993	0.057291733159706	0.092164962039527
-TR4084|c0_g1_i1	wt_37	wt_GSNO	93.2264707954139	121.352438036668	107.289454416041	-0.380198430346905	0.213412163689062	-1.78152183912463	0.0748272403991533	0.115358662282028
-TR1891|c0_g1_i1	wt_37	wt_GSNO	107.628573623499	135.399287466928	121.513930545214	-0.328810062058933	0.189329296532127	-1.73670989161013	0.0824383909023624	0.122008818535496
-TR4669|c0_g2_i1	wt_37	wt_GSNO	0	167.096667347181	83.5483336735905	-3.46077834317638	2.04233842282563	-1.69451757088734	0.0901669757000038	0.128314542342313
-TR1837|c2_g1_i1	wt_37	wt_GSNO	0.308903905435236	2.22601224010275	1.26745807276899	-2.41951712666755	1.51166579847997	-1.60056351681732	0.1094736282342	0.150019416469089
-TR5075|c0_g1_i1	wt_37	wt_GSNO	15.8633018853512	9.23822794034992	12.5507649128506	0.764028730403883	0.508108615055784	1.50367206491864	0.132665825459353	0.172493073735055
-TR4859|c0_g1_i1	wt_37	wt_GSNO	7.32690480813971	3.17910584569163	5.25300532691567	1.18248087647214	0.791530422232021	1.49391715499409	0.135197274008557	0.172493073735055
-TR939|c0_g1_i1	wt_37	wt_GSNO	84.2568220960088	96.9171174594069	90.5869697777078	-0.202690605185084	0.202556787736977	-1.00066064163834	0.316990901598642	0.384256032989688
-TR2278|c0_g1_i1	wt_37	wt_GSNO	486.5272515724	448.140178813055	467.333715192727	0.118822806572317	0.119966033346418	0.99047041281427	0.321944243856225	0.384256032989688
-TR2011|c5_g1_i1	wt_37	wt_GSNO	5.60408627995835	7.88255079488408	6.74331853742122	-0.48861876789566	0.691406970296359	-0.706702114510391	0.479751615248569	0.554712805131158
-TR2182|c3_g2_i6	wt_37	wt_GSNO	2.24974854180929	1.3031439398571	1.77644624083319	0.779605221657958	1.28583289420755	0.606303684693354	0.544313112275579	0.605163179078445
-TR3249|c0_g1_i1	wt_37	wt_GSNO	1.12573841927462	2.128954842887	1.62734663108081	-0.761341397480685	1.29336792501876	-0.58865028485196	0.556095894288301	0.605163179078445
-TR1678|c0_g1_i1	wt_37	wt_GSNO	0.595141051681226	0.700100668536423	0.647620860108824	-0.247288262290953	1.73789746083653	-0.14229162989393	0.886849657633351	0.935371730620685
-TR1122|c0_g1_i1	wt_37	wt_GSNO	1.41370386226057	1.3031439398571	1.35842390105883	0.162148276801819	1.43591594510694	0.112923237153511	0.910091413576882	0.935371730620685
-TR1982|c2_g1_i1	wt_37	wt_GSNO	5.73684100209948	5.71221669652109	5.72452884931028	-0.0101267142582557	0.715373046105777	-0.0141558510114153	0.988705642243408	0.988705642243408
+TR4277|c0_g1_i1	wt_37	wt_GSNO	3852.97388871986	161.116814813422	2007.04535176664	4.57661492404411	0.121615845393926	37.6317321909822	0	0
+TR131|c0_g1_i1	wt_37	wt_GSNO	26.1866396538608	1340.30918254958	683.247911101723	-5.68565819121436	0.188173369545147	-30.2149990987446	1.50487696827007e-200	2.48304699764561e-199
+TR4761|c0_g1_i1	wt_37	wt_GSNO	1645.20640957447	193.196157329029	919.201283451752	3.09227622940716	0.143766888218038	21.5089598706302	1.28350063536341e-102	1.41185069889975e-101
+TR3091|c0_g1_i1	wt_37	wt_GSNO	16.7444693227929	328.569936894811	172.657203108802	-4.30529554105297	0.242003292489129	-17.790235400398	8.41257542125902e-71	6.94037472253869e-70
+TR3638|c0_g1_i1	wt_37	wt_GSNO	583.00358519031	183.754416330029	383.37900076017	1.66225356244238	0.144704273829595	11.487245804501	1.5290952692426e-30	1.00920287770012e-29
+TR2487|c0_g1_i1	wt_37	wt_GSNO	342.210853400436	920.407318992504	631.30908619647	-1.42823125318501	0.124766100464837	-11.44727011475	2.42667678803784e-30	1.33467223342081e-29
+TR3788|c0_g1_i1	wt_37	wt_GSNO	19.5075441237117	134.95369713876	77.2306206312357	-2.78185518936858	0.26452057618315	-10.5165928091827	7.24461724546031e-26	3.41531955857415e-25
+TR1479|c0_g1_i1	wt_37	wt_GSNO	129.593534475689	371.064629188207	250.329081831948	-1.51632040995179	0.145721574162902	-10.405599985193	2.33778717307793e-25	9.64337208894648e-25
+TR2107|c1_g1_i1	wt_37	wt_GSNO	48.9228907410258	7.40521775805688	28.1640542495414	2.72565745131165	0.439033221898883	6.20831708252687	5.35550100392654e-10	1.96368370143973e-09
+TR3854|c0_g1_i1	wt_37	wt_GSNO	1573.69549271337	2374.56159860719	1974.12854566028	-0.593952181868433	0.11125243839418	-5.33877900063632	9.35746226940931e-08	3.08796254890507e-07
+TR2122|c0_g2_i2	wt_37	wt_GSNO	119.534640490118	199.143666337033	159.339153413576	-0.73989736621081	0.168946597067547	-4.37947481070002	1.18965671308434e-05	3.56897013925302e-05
+TR1449|c0_g1_i1	wt_37	wt_GSNO	180.814952011467	104.755290736358	142.785121373912	0.785811747593425	0.186397685526418	4.2157806057203	2.48915666101662e-05	6.6882655779165e-05
+TR4163|c0_g1_i1	wt_37	wt_GSNO	347.283468916919	232.772947466212	290.028208191566	0.5773903092812	0.137377906430929	4.20293425836637	2.63477128827014e-05	6.6882655779165e-05
+TR2672|c0_g1_i1	wt_37	wt_GSNO	18.3155337236093	2.26581902751323	10.2906763755613	2.9857084616452	0.761209385049731	3.92232218924907	8.76996107235725e-05	0.000206720510991278
+TR5055|c0_g2_i1	wt_37	wt_GSNO	23.3590211688541	5.52768338415684	14.4433522765055	2.08513896568298	0.577312677901881	3.61180179389265	0.00030407694239889	0.000668969273277559
+TR2844|c0_g1_i1	wt_37	wt_GSNO	158.206282615139	231.762548186068	194.984415400603	-0.551426184671915	0.155135532159318	-3.55448024702441	0.000378726959348647	0.000781124353656584
+TR127|c1_g1_i1	wt_37	wt_GSNO	13.461799216177	1.21881296083961	7.34030608850831	3.52517488060096	1.00261297574214	3.51598769005717	0.00043812129728732	0.000850470753557739
+TR5212|c0_g1_i1	wt_37	wt_GSNO	65.7079302129484	107.875371765755	86.7916509893515	-0.715754705745061	0.210644233010842	-3.39793164766215	0.000678973819799399	0.0012447853362989
+TR1894|c2_g1_i1	wt_37	wt_GSNO	13.3497721959996	2.96749216411516	8.15863218005739	2.116499695166	0.744618031030184	2.84239651333424	0.00447757649596373	0.00777684338772647
+TR24|c0_g1_i1	wt_37	wt_GSNO	69.9065207344592	41.2394742844514	55.5729975094553	0.763675526543044	0.270944643994893	2.81856660933825	0.00482386011442888	0.00795936918880766
+TR4669|c0_g2_i1	wt_37	wt_GSNO	0	167.096667347181	83.5483336735905	-10.0466852501689	3.90738405199054	-2.57120495873725	0.0101345328521317	0.0159256944819212
+TR2779|c0_g1_i1	wt_37	wt_GSNO	155.915506826481	205.619872596257	180.767689711369	-0.403209397282846	0.18950756245476	-2.12766916559914	0.033364523163095	0.0500467847446426
+TR3807|c0_g1_i1	wt_37	wt_GSNO	3.48709246029019	0.350050334268211	1.9185713972792	3.04810928058763	1.5874506366217	1.92012854464212	0.0548416645360559	0.0786858665082542
+TR1492|c0_g1_i2	wt_37	wt_GSNO	1640.89375005483	1435.64893261411	1538.27134133447	0.192601921423703	0.101311986688049	1.90107733270247	0.0572918841322824	0.0787763406818883
+TR4084|c0_g1_i1	wt_37	wt_GSNO	93.2264707954139	121.352438036668	107.289454416041	-0.381231151484282	0.21399248813321	-1.78151651401411	0.0748281095286258	0.0987731045777861
+TR1891|c0_g1_i1	wt_37	wt_GSNO	107.628573623499	135.399287466928	121.513930545214	-0.329513668205708	0.189733845104182	-1.7367152814764	0.0824374390602291	0.104632134191829
+TR1837|c2_g1_i1	wt_37	wt_GSNO	0.308903905435236	2.22601224010275	1.26745807276899	-2.87715913917267	1.7927876855897	-1.60485213184979	0.108526350064413	1
+TR5075|c0_g1_i1	wt_37	wt_GSNO	15.8633018853512	9.23822794034992	12.5507649128506	0.776103293030194	0.516446682273215	1.5027752518693	0.13289700980576	0.16070937436521
+TR4859|c0_g1_i1	wt_37	wt_GSNO	7.32690480813971	3.17910584569163	5.25300532691567	1.23041974278822	0.82607009598701	1.48948587869905	0.13635946915836	0.16070937436521
+TR939|c0_g1_i1	wt_37	wt_GSNO	84.2568220960088	96.9171174594069	90.5869697777078	-0.203187486812458	0.203052234052517	-1.00066609835923	0.316988262617008	0.354139456794138
+TR2278|c0_g1_i1	wt_37	wt_GSNO	486.5272515724	448.140178813055	467.333715192727	0.118924512672215	0.120068895863502	0.990468945491189	0.321944960721944	0.354139456794138
+TR2011|c5_g1_i1	wt_37	wt_GSNO	5.60408627995835	7.88255079488408	6.74331853742122	-0.50342873702063	0.712267625142964	-0.706797163383052	0.479692537619295	0.510640443272153
+TR2182|c3_g2_i6	wt_37	wt_GSNO	2.24974854180929	1.3031439398571	1.77644624083319	0.878491642458712	1.45214866443311	0.604959852923637	0.545205672528741	0.562243349795264
+TR3249|c0_g1_i1	wt_37	wt_GSNO	1.12573841927462	2.128954842887	1.62734663108081	-0.858277190977929	1.45820967054459	-0.588582841216099	0.556141147160533	1
+TR1678|c0_g1_i1	wt_37	wt_GSNO	0.595141051681226	0.700100668536423	0.647620860108824	-0.322353878735801	2.26929239960538	-0.142050393678601	0.887040200834538	1
+TR1122|c0_g1_i1	wt_37	wt_GSNO	1.41370386226057	1.3031439398571	1.35842390105883	0.189589394350501	1.67633508161709	0.113097552171736	0.909953215626095	1
+TR1982|c2_g1_i1	wt_37	wt_GSNO	5.73684100209948	5.71221669652109	5.72452884931028	-0.0104554076697487	0.738553450989727	-0.0141566025529196	0.988705042660126	0.988705042660126
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,7 @@
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR4277|c0_g1_i1	wt_37	wt_GSNO	3852.97388871986	161.116814813422	2007.04535176664	4.57260002898197	0.121471586836965	37.6433711623376	0	0	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4761|c0_g1_i1	wt_37	wt_GSNO	1645.20640957447	193.196157329029	919.201283451752	3.08848040390227	0.143569117275296	21.5121501233448	1.19819880470067e-102	1.47777852579749e-101	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR2107|c1_g1_i1	wt_37	wt_GSNO	48.9228907410258	7.40521775805688	28.1640542495414	2.69488884014666	0.432209832999676	6.23514005094067	4.51374085119887e-10	1.85564901660398e-09	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR2672|c0_g1_i1	wt_37	wt_GSNO	18.3155337236093	2.26581902751323	10.2906763755613	2.88788179640237	0.725539563189254	3.98032298019437	6.88216980025882e-05	0.000181885916149697	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR127|c1_g1_i1	wt_37	wt_GSNO	13.461799216177	1.21881296083961	7.34030608850831	3.33150202228086	0.915899815581865	3.63740877070095	0.000275394687501815	0.000667511143840185	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR5055|c0_g2_i1	wt_37	wt_GSNO	23.3590211688541	5.52768338415684	14.4433522765055	2.04460941512382	0.563987307210913	3.62527558507482	0.000288653467606567	0.000667511143840185	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,4 @@
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR131|c0_g1_i1	wt_37	wt_GSNO	26.1866396538608	1340.30918254958	683.247911101723	-5.67373033438939	0.187375754459626	-30.2799599166492	2.10486694333775e-201	3.89400384517483e-200	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR3091|c0_g1_i1	wt_37	wt_GSNO	16.7444693227929	328.569936894811	172.657203108802	-4.29037251456992	0.240582794801874	-17.8332474610379	3.90090325510546e-71	3.60833551097255e-70	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR3788|c0_g1_i1	wt_37	wt_GSNO	19.5075441237117	134.95369713876	77.2306206312357	-2.77036684869735	0.263152237265066	-10.527620351967	6.4442989603998e-26	3.40627230763989e-25	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,39 +1,38 @@
-logFC	logCPM	PValue	FDR
-TR131|c0_g1_i1	5.8364197685119	16.0402624962907	0	0
-TR4277|c0_g1_i1	-4.41329137350676	17.4523259866001	0	0
-TR3091|c0_g1_i1	4.45193883524837	14.0450613692144	2.75977672027703e-191	3.0023764016608e-190
-TR4761|c0_g1_i1	-2.92753980838104	16.3343761538543	3.16039621227453e-191	3.0023764016608e-190
-TR2487|c0_g1_i1	1.58705373680526	15.8895982491351	1.69098562804069e-123	1.28514907731092e-122
-TR1479|c0_g1_i1	1.67068054401246	14.5625418524933	4.82942248775202e-81	3.05863424224295e-80
-TR3638|c0_g1_i1	-1.49936398500381	15.1049693447894	1.31792237756209e-64	7.15443576390849e-64
-TR3854|c0_g1_i1	0.756865722480515	17.5147652035186	8.35417282711821e-40	3.96823209288115e-39
-TR2122|c0_g2_i2	0.903942128151819	13.8996874045924	3.62505920095794e-13	1.53058055151558e-12
-TR2844|c0_g1_i1	0.707836713891037	14.1854217777842	1.87464339893047e-12	7.1236449159358e-12
-TR3788|c0_g1_i1	2.92403132462783	12.8779140660683	1.50355808369265e-09	5.19410974366551e-09
-TR4669|c0_g2_i1	10.5374101870061	13.0322839834498	3.83881845042015e-08	1.21562584263305e-07
-TR2672|c0_g1_i1	-2.77697626464917	10.2324144831548	6.6653206315345e-08	1.9483244922947e-07
-TR4163|c0_g1_i1	-0.420124679057253	14.7293558096347	2.6407759845512e-06	7.16782052949613e-06
-TR2107|c1_g1_i1	-2.54740509831049	11.4796217709789	1.31520100526586e-05	3.33184254667352e-05
-TR2779|c0_g1_i1	0.57151150266807	14.0680960027645	7.44562831370785e-05	0.000176833672450561
-TR127|c1_g1_i1	-3.25307512484374	9.84850588284066	0.000331345441643876	0.000740654516615722
-TR1894|c2_g1_i1	-1.90241917506329	9.93135664117576	0.00432077639530722	0.00912163905675968
-TR5055|c0_g2_i1	-1.8950478385132	10.598211984773	0.00591755208579545	0.0118351041715909
-TR2090|c0_g1_i1	6.41050251489574	9.11635750687386	0.0113096900461153	0.021488411087619
-TR5212|c0_g1_i1	0.867439938079617	13.0331405503531	0.0317111501604761	0.0573820812427663
-TR3807|c0_g1_i1	-2.67963301995355	8.56046890206839	0.0557212159288941	0.0962457366044534
-TR1449|c0_g1_i1	-0.636836241811875	13.7146214195087	0.0845994280568489	0.139772968093924
-TR4084|c0_g1_i1	0.527023803952886	13.333880353991	0.19596368831627	0.301997237380275
-TR1891|c0_g1_i1	0.481345196849859	13.5019985083809	0.198682393013339	0.301997237380275
-TR24|c0_g1_i1	-0.590671163985234	12.3854267629296	0.21115333494008	0.308608720297039
-TR1837|c2_g1_i1	2.67943439258847	8.19914223144978	0.242162966500684	0.336820885113627
-TR4859|c0_g1_i1	-1.04273446956489	9.43870802835889	0.248183810083725	0.336820885113627
-TR939|c0_g1_i1	0.361607908864682	13.0838256643577	0.341542524228359	0.447538480023367
-TR2011|c5_g1_i1	0.672074276530526	9.63297397547156	0.357699118838244	0.453085550528442
-TR5075|c0_g1_i1	-0.617596452044795	10.4317228965746	0.378826401739151	0.464367847293153
-TR3249|c0_g1_i1	0.936067544593607	8.34110243846743	0.532174466327564	0.631957178763983
-TR1492|c0_g1_i2	-0.0311770185465736	17.1360846492483	0.562063331952301	0.647224442854165
-TR2278|c0_g1_i1	0.0373157391528861	15.4251088322423	0.63557189922311	0.710345063837593
-TR2182|c3_g2_i6	-0.665499179094881	8.45651702709919	0.835363486459349	0.906966071013008
-TR1982|c2_g1_i1	0.176241441184615	9.49445846907393	0.904611213246767	0.954867391760477
-TR1678|c0_g1_i1	0.476522568809639	7.93710096737952	1	1
-TR1122|c0_g1_i1	-0.015204817268041	8.26206767263358	1	1
+sampleA	sampleB	logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	wt_37	wt_GSNO	-5.83641794955382	16.0393491449056	0	0
+TR4277|c0_g1_i1	wt_37	wt_GSNO	4.41329536892161	17.453649857324	0	0
+TR3091|c0_g1_i1	wt_37	wt_GSNO	-4.45192710783926	14.0403115023365	4.66239713643175e-192	5.75028980159916e-191
+TR4761|c0_g1_i1	wt_37	wt_GSNO	2.92754337500687	16.3361488759619	3.05265683396309e-191	2.82370757141586e-190
+TR2487|c0_g1_i1	wt_37	wt_GSNO	-1.58705168340508	15.8893887856701	9.57106937146597e-124	7.08259133488482e-123
+TR1479|c0_g1_i1	wt_37	wt_GSNO	-1.67065982572176	14.5610246448295	4.39649357092684e-84	2.71117103540489e-83
+TR3638|c0_g1_i1	wt_37	wt_GSNO	1.49937182627392	15.1071990563814	1.60652562072048e-64	8.49163542380826e-64
+TR3854|c0_g1_i1	wt_37	wt_GSNO	-0.756864683109858	17.5153338325952	9.14141417630157e-40	4.22790405653948e-39
+TR2122|c0_g2_i2	wt_37	wt_GSNO	-0.90394318029981	13.8984589155106	3.98287653266084e-13	1.63740479676057e-12
+TR2844|c0_g1_i1	wt_37	wt_GSNO	-0.707834005847516	14.1849675326065	1.90004997002049e-12	7.0301848890758e-12
+TR3788|c0_g1_i1	wt_37	wt_GSNO	-2.92402824575823	12.8707284018497	1.35908019280542e-09	4.57145155761824e-09
+TR4669|c0_g2_i1	wt_37	wt_GSNO	-10.5373989771184	13.0207784411552	2.87822490296537e-08	8.87452678414323e-08
+TR2672|c0_g1_i1	wt_37	wt_GSNO	2.77705541360002	10.2430402179839	7.41806563943484e-08	2.11129560506992e-07
+TR4163|c0_g1_i1	wt_37	wt_GSNO	0.420123134789911	14.7306522277754	2.74345107938324e-06	7.25054928122714e-06
+TR127|c1_g1_i1	wt_37	wt_GSNO	3.26487561187968	9.85808314705506	6.1191913603037e-06	1.50940053554158e-05
+TR2107|c1_g1_i1	wt_37	wt_GSNO	2.54741701164587	11.489948731934	1.24782096095324e-05	2.88558597220436e-05
+TR2779|c0_g1_i1	wt_37	wt_GSNO	-0.571512278204146	14.0677635717422	7.39487278515011e-05	0.000160947231206208
+TR1894|c2_g1_i1	wt_37	wt_GSNO	1.88989717290856	9.93884262525918	0.00064827406279645	0.00133256335130381
+TR5055|c0_g2_i1	wt_37	wt_GSNO	1.89504810994952	10.6064804346292	0.00584438080176016	0.011381162613954
+TR3807|c0_g1_i1	wt_37	wt_GSNO	2.66606066906632	8.56455983886691	0.0188051214716541	0.0347894747225602
+TR5212|c0_g1_i1	wt_37	wt_GSNO	-0.867441722907523	13.0312878134755	0.0313380642877521	0.055214684697468
+TR1449|c0_g1_i1	wt_37	wt_GSNO	0.636828244112651	13.716963541734	0.0836258106887223	0.140643408885578
+TR1837|c2_g1_i1	wt_37	wt_GSNO	-2.70136949048315	8.19724487849862	0.11443273811818	0.184087448277072
+TR4859|c0_g1_i1	wt_37	wt_GSNO	1.06021338602227	9.44252758756623	0.17021260004507	0.262411091736149
+TR4084|c0_g1_i1	wt_37	wt_GSNO	-0.527027354857722	13.3333941866224	0.195100037539558	0.280916147575458
+TR1891|c0_g1_i1	wt_37	wt_GSNO	-0.481344817930584	13.5015018099629	0.197400536134106	0.280916147575458
+TR24|c0_g1_i1	wt_37	wt_GSNO	0.590686928315332	12.3882336221811	0.209814398393357	0.287523434835341
+TR2011|c5_g1_i1	wt_37	wt_GSNO	-0.668008806764204	9.63014074618193	0.239244885423374	0.316145027166602
+TR939|c0_g1_i1	wt_37	wt_GSNO	-0.361607139894815	13.0833886152319	0.340252678428006	0.434115486270215
+TR5075|c0_g1_i1	wt_37	wt_GSNO	0.617585416067661	10.4358029661318	0.377913209145196	0.466092957945741
+TR1492|c0_g1_i2	wt_37	wt_GSNO	0.0311900896664335	17.1368189470585	0.559289231968699	0.657620159615942
+TR3249|c0_g1_i1	wt_37	wt_GSNO	-0.894241538356016	8.33957569586088	0.568752570478653	0.657620159615942
+TR2278|c0_g1_i1	wt_37	wt_GSNO	-0.0373200220187202	15.4258149088647	0.636489077475997	0.713639268685208
+TR2182|c3_g2_i6	wt_37	wt_GSNO	0.714549920613349	8.45775163335771	0.790296098133788	0.860028106792652
+TR1982|c2_g1_i1	wt_37	wt_GSNO	-0.181275971858276	9.49467590956657	0.873422282667325	0.923332127391172
+TR1678|c0_g1_i1	wt_37	wt_GSNO	-0.476606391142577	7.93769527756871	1	1
+TR1122|c0_g1_i1	wt_37	wt_GSNO	0.0647357997613641	8.26206759454538	1	1
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,39 +1,38 @@
-logFC	logCPM	PValue	FDR
-TR131|c0_g1_i1	5.8235943392439	16.1127963113785	7.14846919291531e-10	2.71641829330782e-08
-TR4277|c0_g1_i1	-4.41182125975734	17.3835558041266	1.56187740933885e-09	2.96756707774382e-08
-TR3091|c0_g1_i1	4.43711915085412	14.1189484156579	4.80332538807657e-08	5.96619459206176e-07
-TR2487|c0_g1_i1	1.58597331690052	15.926957585609	6.28020483374923e-08	5.96619459206176e-07
-TR4761|c0_g1_i1	-2.92047098366841	16.2714320125634	5.50582910815067e-07	4.18443012219451e-06
-TR1479|c0_g1_i1	1.67737907773679	14.6004783880878	9.51214752241748e-07	5.52604916020242e-06
-TR3638|c0_g1_i1	-1.50273266496817	15.0596817330556	1.02518921423282e-06	5.52604916020242e-06
-TR3788|c0_g1_i1	2.93902285611693	12.9382150715361	2.41689084349911e-06	1.02046502281074e-05
-TR3854|c0_g1_i1	0.759398996973938	17.5343629610585	1.16337877056893e-06	5.52604916020242e-06
-TR2107|c1_g1_i1	-2.46238704341773	11.2600018185657	0.000160625103091043	0.000554886719769058
-TR2122|c0_g2_i2	0.898555189960494	13.9141616710754	0.000116065228333624	0.000441047867667773
-TR2844|c0_g1_i1	0.712285451514242	14.1964395706942	0.000226456956836179	0.0007171136966479
-TR5212|c0_g1_i1	0.877383155201317	13.0382243238454	0.00044264831250554	0.00129389506732389
-TR4163|c0_g1_i1	-0.417753044994067	14.7100536369854	0.00073550773195026	0.00199637812957928
-TR1449|c0_g1_i1	-0.639430683731338	13.6750299459863	0.0021688744394372	0.00549448191324091
-TR2672|c0_g1_i1	-2.89090970573392	9.81450205355949	0.0110308904582196	0.0220617809164392
-TR127|c1_g1_i1	-3.10441694967501	9.33201892428652	0.0147505107490706	0.0271381068158418
-TR939|c0_g1_i1	0.363392391144623	13.0700139113805	0.00528218330196852	0.0125451853421752
-TR5055|c0_g2_i1	-1.80082179647401	10.290740057161	0.014997374819281	0.0271381068158418
-TR1894|c2_g1_i1	-1.81920882927282	9.4761161835092	0.0211021355265418	0.0348643978264604
-TR1891|c0_g1_i1	0.477106166889499	13.4994625375761	0.00640932243854848	0.0143267207449907
-TR1837|c2_g1_i1	2.21852868850051	7.02301103616459	0.041457300582048	0.063015096884713
-TR3807|c0_g1_i1	-1.9168529396959	7.35599058475032	0.0566225608328877	0.0827560504480666
-TR2779|c0_g1_i1	0.600059279980753	14.0739938889057	0.00964636468216327	0.0203645476623447
-TR24|c0_g1_i1	-0.588697529952342	12.3096839182028	0.0194904179372949	0.0336652673462366
-TR4859|c0_g1_i1	-1.06821251099455	8.91301871295058	0.111617387620425	0.157091138132451
-TR2090|c0_g1_i1	2.22339391910091	8.98366602727699	0.254495907488744	0.322361482819076
-TR4084|c0_g1_i1	0.567566096899832	13.3297126444574	0.036433281659912	0.0576860292948607
-TR2182|c3_g2_i6	-1.0316496616205	7.37334712818428	0.34572838664377	0.423796086853654
-TR2011|c5_g1_i1	0.791574287810665	9.32879226678442	0.161547389819689	0.211682786660282
-TR5075|c0_g1_i1	-0.550289601556128	10.1785868671389	0.12853444928267	0.174439609740767
-TR1678|c0_g1_i1	0.331221243897688	5.95523974949609	0.7547763751788	0.806418050624271
-TR4669|c0_g2_i1	6.27373933776222	13.1239272719772	0.48073138273468	0.553569471027814
-TR1122|c0_g1_i1	-0.199192308627843	7.01379133029712	0.87736931102229	0.87736931102229
-TR3249|c0_g1_i1	0.258869539778469	7.31927198802943	0.798677928444158	0.820263818402108
-TR1982|c2_g1_i1	0.132112224684827	9.08491674138301	0.763974995328257	0.806418050624271
-TR2278|c0_g1_i1	0.0407550618622219	15.423513715505	0.613273487399665	0.685423309446684
-TR1492|c0_g1_i2	-0.0324123498367541	17.1356104672946	0.389074079094509	0.462025468924729
+sampleA	sampleB	logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	wt_37	wt_GSNO	-5.82360148900389	16.1142242655408	6.54502972918692e-10	2.42166099979916e-08
+TR4277|c0_g1_i1	wt_37	wt_GSNO	4.41183386172098	17.3836256000268	1.7102544921365e-09	3.16397081045253e-08
+TR3091|c0_g1_i1	wt_37	wt_GSNO	-4.43700179801176	14.1203688767724	4.42033048679943e-08	5.45174093371929e-07
+TR2487|c0_g1_i1	wt_37	wt_GSNO	-1.58598083708684	15.9280757073272	7.01720228399608e-08	6.49091211269637e-07
+TR4761|c0_g1_i1	wt_37	wt_GSNO	2.92043321768346	16.2716301848411	5.72725934421127e-07	4.23817191471634e-06
+TR1479|c0_g1_i1	wt_37	wt_GSNO	-1.67738254434993	14.6016057367881	1.03919750932427e-06	5.8615543150164e-06
+TR3638|c0_g1_i1	wt_37	wt_GSNO	1.50288215872986	15.0600281889274	1.12469315856867e-06	5.8615543150164e-06
+TR3788|c0_g1_i1	wt_37	wt_GSNO	-2.93907650045598	12.9393872783943	2.35975448958169e-06	9.70121290161359e-06
+TR3854|c0_g1_i1	wt_37	wt_GSNO	-0.759397690410038	17.5353083640786	1.26736309513868e-06	5.8615543150164e-06
+TR2107|c1_g1_i1	wt_37	wt_GSNO	2.46233758474327	11.260249244859	0.000163907571391062	0.000551325467406299
+TR2122|c0_g2_i2	wt_37	wt_GSNO	-0.898543060702643	13.9151768182402	0.000124408949544541	0.000460313113314803
+TR2844|c0_g1_i1	wt_37	wt_GSNO	-0.712202725875737	14.1973066750225	0.000243984033514546	0.000752284103336518
+TR5212|c0_g1_i1	wt_37	wt_GSNO	-0.87701850957337	13.0391017777502	0.000473838954429694	0.00134861856260759
+TR4163|c0_g1_i1	wt_37	wt_GSNO	0.417694804483349	14.7107025605232	0.000805848497363634	0.00212974245731817
+TR2672|c0_g1_i1	wt_37	wt_GSNO	2.90562993555483	9.81450205355949	0.00822748279906008	0.0169120479758457
+TR1449|c0_g1_i1	wt_37	wt_GSNO	0.640011354440497	13.6755402195434	0.00227354555819909	0.00560807904355776
+TR127|c1_g1_i1	wt_37	wt_GSNO	3.09466453837236	9.33233275488244	0.00997545255499303	0.0184545872267371
+TR1894|c2_g1_i1	wt_37	wt_GSNO	1.8273232048322	9.47625819175118	0.0170307015491222	0.0286425435144327
+TR5055|c0_g2_i1	wt_37	wt_GSNO	1.79897959483123	10.2910629958573	0.0144290410083875	0.025422596062397
+TR939|c0_g1_i1	wt_37	wt_GSNO	-0.363394684962815	13.0708604932728	0.00579686595094712	0.0134052525115652
+TR1837|c2_g1_i1	wt_37	wt_GSNO	-2.21418127698954	7.02378849272624	0.0306005987832276	0.0471759231241425
+TR1891|c0_g1_i1	wt_37	wt_GSNO	-0.477062796219233	13.500309435849	0.00675073796972544	0.0146927826399907
+TR3807|c0_g1_i1	wt_37	wt_GSNO	1.91879773659378	7.35599058475032	0.0402625583382777	0.0572967176352414
+TR2779|c0_g1_i1	wt_37	wt_GSNO	-0.600036558858359	14.0748557225205	0.00991998269314111	0.0184545872267371
+TR24|c0_g1_i1	wt_37	wt_GSNO	0.588796779058576	12.310400953631	0.0185008090691583	0.0297621711112546
+TR4859|c0_g1_i1	wt_37	wt_GSNO	1.06036244689068	8.9138577436531	0.104550838513832	0.143273371296733
+TR4084|c0_g1_i1	wt_37	wt_GSNO	-0.567278869966665	13.330468891507	0.0372234219214301	0.0550906644437166
+TR2011|c5_g1_i1	wt_37	wt_GSNO	-0.789577978066661	9.33004998835934	0.161975973261362	0.206659000367944
+TR2182|c3_g2_i6	wt_37	wt_GSNO	1.02218394394404	7.37517597546907	0.329234058043314	0.406055338253421
+TR5075|c0_g1_i1	wt_37	wt_GSNO	0.549449880041588	10.1791103984097	0.127566698813275	0.168570280574684
+TR4669|c0_g2_i1	wt_37	wt_GSNO	-6.27345157840298	13.126293325041	0.423017017822531	0.489113426857301
+TR1678|c0_g1_i1	wt_37	wt_GSNO	-0.330222398445961	5.95523974949609	0.735881722270124	0.79829094077818
+TR1122|c0_g1_i1	wt_37	wt_GSNO	0.193564460109425	7.01613737702005	0.875819231521416	0.875819231521416
+TR3249|c0_g1_i1	wt_37	wt_GSNO	-0.276543877903423	7.32180296800742	0.776715509946338	0.79829094077818
+TR1982|c2_g1_i1	wt_37	wt_GSNO	-0.131251756802268	9.08566155151058	0.763275890632561	0.79829094077818
+TR2278|c0_g1_i1	wt_37	wt_GSNO	-0.0407242590322052	15.424279874284	0.616230913043451	0.69092556916993
+TR1492|c0_g1_i2	wt_37	wt_GSNO	0.0323916193661019	17.1363857315734	0.39613877470297	0.472810795613223
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,39 +1,39 @@
 sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
-TR4277|c0_g1_i1	wt_37	wt_ph8	4705.34614971641	162.902721493704	2434.12443560506	4.84804012036106	0.130783542648097	37.0691909868646	8.81406568413535e-301	3.34934495997143e-299
-TR131|c0_g1_i1	wt_37	wt_ph8	32.0461070493257	1436.30905989883	734.177583474076	-5.48335951236111	0.197548955320184	-27.7569653733364	1.43583336471356e-169	2.72808339295576e-168
-TR3091|c0_g1_i1	wt_37	wt_ph8	20.4914097091341	321.651020117047	171.071214913091	-3.97084930318667	0.245881056057371	-16.1494722971263	1.14537343838751e-58	1.45080635529084e-57
-TR4761|c0_g1_i1	wt_37	wt_ph8	2012.6141923276	384.620292965437	1198.61724264652	2.38432084623308	0.148099583891604	16.0994432501458	2.57410332221217e-58	2.44539815610156e-57
-TR5075|c0_g1_i1	wt_37	wt_ph8	19.3833722195684	136.98672801182	78.1850501156942	-2.80247674171473	0.269715041166808	-10.3905096637956	2.73885623424733e-25	2.08153073802797e-24
-TR2779|c0_g1_i1	wt_37	wt_ph8	191.51955185349	1058.15934185376	624.839446853626	-2.45909834872711	0.247058756007882	-9.95349603658112	2.43476309780354e-23	1.54201662860891e-22
-TR1891|c0_g1_i1	wt_37	wt_ph8	131.416087212132	376.595292171713	254.005689691923	-1.51504907455703	0.163541333568612	-9.26401320997792	1.96889433896152e-20	1.06882835543625e-19
-TR1492|c0_g1_i2	wt_37	wt_ph8	2006.11782336441	890.823502721036	1448.47066304272	1.17018000582475	0.127273970398445	9.19418167093695	3.77859650812701e-20	1.79483334136033e-19
-TR2487|c0_g1_i1	wt_37	wt_ph8	418.818667162757	965.862817209246	692.340742186001	-1.2054117169244	0.138501088570193	-8.70326529104133	3.22468912161225e-18	1.36153540690295e-17
-TR3638|c0_g1_i1	wt_37	wt_ph8	713.131183384274	326.063958913919	519.597571149096	1.12815426477841	0.141332330235517	7.98228022490288	1.43654437320665e-15	5.45886861818526e-15
-TR2107|c1_g1_i1	wt_37	wt_ph8	59.5986596731862	1.89840873462066	30.7485342039034	4.82151434610286	0.613172060454942	7.86323229164347	3.74345886500564e-15	1.29319488063831e-14
-TR2122|c0_g2_i2	wt_37	wt_ph8	146.135958637131	360.821667264163	253.478812950647	-1.30371385707787	0.169650604759161	-7.68469914344628	1.53356953387865e-14	4.85630352394907e-14
-TR1479|c0_g1_i1	wt_37	wt_ph8	158.005105094407	334.827472148091	246.416288621249	-1.0787542477693	0.165556938369539	-6.51591083039607	7.22498877976404e-11	2.1119197971618e-10
-TR24|c0_g1_i1	wt_37	wt_ph8	85.6614643869141	199.923709280262	142.792586833588	-1.2279226670979	0.196562275775691	-6.24699048814003	4.18436531652641e-10	1.13575630020003e-09
-TR4163|c0_g1_i1	wt_37	wt_ph8	424.593720981574	227.471218917767	326.03246994967	0.900981410818221	0.155876696706134	5.78009048085484	7.46604610022994e-09	1.89139834539158e-08
-TR1449|c0_g1_i1	wt_37	wt_ph8	220.782434528097	117.26089394399	169.021664236043	0.914395516820343	0.174920034977504	5.22750591113215	1.71811907274331e-07	4.08053279776536e-07
-TR2278|c0_g1_i1	wt_37	wt_ph8	594.657329919233	348.341653317169	471.499491618201	0.772496794598277	0.157892732036131	4.89254182023719	9.95419556957436e-07	2.2250554802578e-06
-TR5055|c0_g2_i1	wt_37	wt_ph8	28.6665933385886	6.05959103586122	17.3630921872249	2.18372312866756	0.505600668447204	4.31906693354301	1.5669025864333e-05	3.30790546024808e-05
-TR127|c1_g1_i1	wt_37	wt_ph8	16.3791628279609	1.58772512712498	8.98344397754296	3.22742307122337	0.758365755070441	4.25576056097574	2.08339575851481e-05	4.16679151702962e-05
-TR1894|c2_g1_i1	wt_37	wt_ph8	16.2826445742552	1.67571344127509	8.97917900776516	3.18830464179373	0.7590595028564	4.20033558607184	2.66519649541344e-05	5.06387334128554e-05
-TR2672|c0_g1_i1	wt_37	wt_ph8	22.3129914439134	7.89947501226409	15.1062332280887	1.46563545973546	0.482353842293509	3.0385068620302	0.00237753690029721	0.00429545997952877
-TR4859|c0_g1_i1	wt_37	wt_ph8	8.91205730249659	1.28188505334354	5.09697117792006	2.65126611500267	0.876469721997014	3.02493748325022	0.00248684525130613	0.00429545997952877
-TR1678|c0_g1_i1	wt_37	wt_ph8	0.738899982352077	7.85275634721875	4.29582816478541	-3.18849648433777	1.0594001628342	-3.00971870327794	0.00261489744098202	0.00432026533727463
-TR4084|c0_g1_i1	wt_37	wt_ph8	113.2594381118	173.837287636503	143.548362874151	-0.608939120027998	0.203268581921877	-2.99573654851409	0.00273782859610482	0.00433489527716597
-TR3807|c0_g1_i1	wt_37	wt_ph8	4.23896204531587	0.352255997713617	2.29560902151474	3.15525660545126	1.31164110647326	2.4055792319098	0.0161468501576278	0.0245432122395943
-TR3249|c0_g1_i1	wt_37	wt_ph8	1.36481976577862	4.37661229401476	2.87071602989669	-1.55893212196469	1.01682768784581	-1.53313303777885	0.125243078950272	0.176625758092245
-TR1859|c3_g1_i1	wt_37	wt_ph8	0.361569353912422	2.25550826604853	1.30853880998047	-2.19284922770108	1.43126836745787	-1.53210206943641	0.125497249170806	0.176625758092245
-TR2090|c0_g1_i1	wt_37	wt_ph8	0	5.87877087384675	2.93938543692337	-2.86225136793822	1.9729684338102	-1.45073348305458	0.146854088052773	0.19930197664305
-TR1982|c2_g1_i1	wt_37	wt_ph8	7.00144976454503	11.520013112092	9.26073143831853	-0.712688609925078	0.555640746749963	-1.28264281209345	0.199617243880331	0.261567423015607
-TR1837|c2_g1_i1	wt_37	wt_ph8	0.377330628439655	1.67813520813222	1.02773291828594	-1.7572235261621	1.52690431775837	-1.15084062945205	0.249797806431129	0.316410554812763
-TR5212|c0_g1_i1	wt_37	wt_ph8	80.2050001877881	94.8352723753388	87.5201362815635	-0.23592411895009	0.215502649097795	-1.09476203628025	0.273620902411289	0.335406267471903
-TR3854|c0_g1_i1	wt_37	wt_ph8	1925.26464813324	2107.16376011081	2016.21420412203	-0.130483054839334	0.130739272627028	-0.998040238540833	0.318259846991125	0.377933568301961
-TR1122|c0_g1_i1	wt_37	wt_ph8	1.69354093201913	0.660517838352177	1.17702938518565	1.18649040337028	1.40558655511286	0.84412475279761	0.398599697111289	0.448776409473292
-TR2844|c0_g1_i1	wt_37	wt_ph8	193.030766468894	213.82243412349	203.426600296192	-0.143791883173722	0.17140940841448	-0.838879758723761	0.401536787423471	0.448776409473292
-TR2011|c5_g1_i1	wt_37	wt_ph8	6.84875389533898	4.81927837273561	5.8340161340373	0.467659672901774	0.714270969980296	0.654737057162879	0.512637061952329	0.556577381548243
-TR2182|c3_g2_i6	wt_37	wt_ph8	2.76248771922916	1.94482465855284	2.353656188891	0.479324872360299	1.02378035563408	0.468191120998245	0.639647921157653	0.675183916777523
-TR3788|c0_g1_i1	wt_37	wt_ph8	23.7579432209456	26.0024682525169	24.8802057367313	-0.124358222905796	0.350105186670918	-0.355202458119214	0.72243792333433	0.741963272613636
-TR939|c0_g1_i1	wt_37	wt_ph8	103.002135647151	102.820214322362	102.911174984756	0.000971215955472081	0.195414642848595	0.00497002651037041	0.996034508905975	0.996034508905975
+TR4277|c0_g1_i1	wt_37	wt_ph8	4705.34614971641	162.902721493704	2434.12443560506	4.85332629705957	0.130960775627329	37.0593887659196	1.26787233139066e-300	4.81791485928452e-299
+TR131|c0_g1_i1	wt_37	wt_ph8	32.0461070493257	1436.30905989883	734.177583474076	-5.49708942597102	0.198466854292743	-27.6977707212645	7.42748041559505e-169	1.41122127896306e-167
+TR3091|c0_g1_i1	wt_37	wt_ph8	20.4914097091341	321.651020117047	171.071214913091	-3.98630633515117	0.247421953542878	-16.1113687693051	2.12272588309166e-58	2.47056970916163e-57
+TR4761|c0_g1_i1	wt_37	wt_ph8	2012.6141923276	384.620292965437	1198.61724264652	2.3876556238738	0.148312557773369	16.0988095662291	2.60059969385434e-58	2.47056970916163e-57
+TR5075|c0_g1_i1	wt_37	wt_ph8	19.3833722195684	136.98672801182	78.1850501156942	-2.81556781738656	0.271397918695418	-10.3743161735385	3.24527446090745e-25	2.46640859028966e-24
+TR2779|c0_g1_i1	wt_37	wt_ph8	191.51955185349	1058.15934185376	624.839446853626	-2.46872482043468	0.248047686960726	-9.95262181511717	2.45625242439133e-23	1.55562653544784e-22
+TR1891|c0_g1_i1	wt_37	wt_ph8	131.416087212132	376.595292171713	254.005689691923	-1.51763504949468	0.1638333296262	-9.26328637132193	1.98234808919548e-20	1.07613181984897e-19
+TR1492|c0_g1_i2	wt_37	wt_ph8	2006.11782336441	890.823502721036	1448.47066304272	1.17138763330801	0.12740597231583	9.19413440371721	3.78025797563847e-20	1.79562253842827e-19
+TR2487|c0_g1_i1	wt_37	wt_ph8	418.818667162757	965.862817209246	692.340742186001	-1.2068861494209	0.138672539999103	-8.70313725722989	3.22833072204789e-18	1.36307297153133e-17
+TR3638|c0_g1_i1	wt_37	wt_ph8	713.131183384274	326.063958913919	519.597571149096	1.12959116050602	0.141514345090045	7.98216717737888	1.43786102301427e-15	5.46387188745423e-15
+TR2122|c0_g2_i2	wt_37	wt_ph8	146.135958637131	360.821667264163	253.478812950647	-1.30611123021679	0.169971549866392	-7.68429323168187	1.53843927144304e-14	5.31460839225778e-14
+TR2107|c1_g1_i1	wt_37	wt_ph8	59.5986596731862	1.89840873462066	30.7485342039034	4.94663101068376	0.648801734442531	7.62425676148051	2.45444399373987e-14	7.77240598017624e-14
+TR1479|c0_g1_i1	wt_37	wt_ph8	158.005105094407	334.827472148091	246.416288621249	-1.08064044509537	0.1658526880096	-6.5156643408325	7.23686413447617e-11	2.11539105469303e-10
+TR24|c0_g1_i1	wt_37	wt_ph8	85.6614643869141	199.923709280262	142.792586833588	-1.2309601921531	0.197065470330035	-6.24645296860761	4.19878369504606e-10	1.13966986008393e-09
+TR4163|c0_g1_i1	wt_37	wt_ph8	424.593720981574	227.471218917767	326.03246994967	0.902378343080323	0.156120482680011	5.78001251078543	7.46950706226027e-09	1.89227512243927e-08
+TR1449|c0_g1_i1	wt_37	wt_ph8	220.782434528097	117.26089394399	169.021664236043	0.916182468982544	0.175267159439457	5.22734819182726	1.71958482582468e-07	4.0840139613336e-07
+TR2278|c0_g1_i1	wt_37	wt_ph8	594.657329919233	348.341653317169	471.499491618201	0.77372548280461	0.158144801146882	4.8925129197639	9.95565784679233e-07	2.22538234222417e-06
+TR5055|c0_g2_i1	wt_37	wt_ph8	28.6665933385886	6.05959103586122	17.3630921872249	2.22056293047175	0.515653625436263	4.30630722045843	1.66002467176804e-05	3.50449652928809e-05
+TR127|c1_g1_i1	wt_37	wt_ph8	16.3791628279609	1.58772512712498	8.98344397754296	3.35782864860774	0.805715621214412	4.16751091848842	3.07943766984562e-05	6.15887533969124e-05
+TR1894|c2_g1_i1	wt_37	wt_ph8	16.2826445742552	1.67571344127509	8.97917900776516	3.31835899440704	0.806156235895963	4.1162728099709	3.85048512190331e-05	7.31592173161629e-05
+TR2672|c0_g1_i1	wt_37	wt_ph8	22.3129914439134	7.89947501226409	15.1062332280887	1.4879160019133	0.490304786216723	3.03467566244728	0.00240794483755529	0.00435723351557623
+TR4084|c0_g1_i1	wt_37	wt_ph8	113.2594381118	173.837287636503	143.548362874151	-0.610546095515356	0.203809508378262	-2.99567032163292	0.00273842322103228	0.00473000374541939
+TR4859|c0_g1_i1	wt_37	wt_ph8	8.91205730249659	1.28188505334354	5.09697117792006	2.79846628921536	0.943303749490582	2.96666507551426	0.00301048704228202	0.00497384815681378
+TR1678|c0_g1_i1	wt_37	wt_ph8	0.738899982352077	7.85275634721875	4.29582816478541	-3.47431884008145	1.21198503063676	-2.8666351087324	0.00414861034620894	0.00656863304816415
+TR3807|c0_g1_i1	wt_37	wt_ph8	4.23896204531587	0.352255997713617	2.29560902151474	3.60257127355045	1.494771199452	2.41011552461754	0.0159474699414718	0.0242401543110371
+TR1859|c3_g1_i1	wt_37	wt_ph8	0.361569353912422	2.25550826604853	1.30853880998047	-2.58650633406891	1.68391965639604	-1.53600340980911	0.124537544060973	0.181135380859875
+TR3249|c0_g1_i1	wt_37	wt_ph8	1.36481976577862	4.37661229401476	2.87071602989669	-1.67837058189371	1.10474169040967	-1.51924254915312	0.12870145482149	0.181135380859875
+TR2090|c0_g1_i1	wt_37	wt_ph8	0	5.87877087384675	2.93938543692337	-4.93100736412614	3.57047444665656	-1.38105101655149	0.167263275059569	0.227000159009415
+TR1982|c2_g1_i1	wt_37	wt_ph8	7.00144976454503	11.520013112092	9.26073143831853	-0.727260398375603	0.567300823658434	-1.28196605406919	0.199854554547715	0.261878381821143
+TR1837|c2_g1_i1	wt_37	wt_ph8	0.377330628439655	1.67813520813222	1.02773291828594	-2.14007669057536	1.85335822648042	-1.15470212935543	0.248212427250959	0.314402407851215
+TR5212|c0_g1_i1	wt_37	wt_ph8	80.2050001877881	94.8352723753388	87.5201362815635	-0.236625075567938	0.21614403033503	-1.09475646956875	0.273623341840838	0.335409257740381
+TR3854|c0_g1_i1	wt_37	wt_ph8	1925.26464813324	2107.16376011081	2016.21420412203	-0.130625245556183	0.13088163358419	-0.998041069468758	0.318259444082768	0.377933089848287
+TR2844|c0_g1_i1	wt_37	wt_ph8	193.030766468894	213.82243412349	203.426600296192	-0.144061748535941	0.17173092225162	-0.838880654963596	0.401536284440308	0.450271927171228
+TR1122|c0_g1_i1	wt_37	wt_ph8	1.69354093201913	0.660517838352177	1.17702938518565	1.3946217378633	1.66721495733336	0.836497856337578	0.402874882205836	0.450271927171228
+TR2011|c5_g1_i1	wt_37	wt_ph8	6.84875389533898	4.81927837273561	5.8340161340373	0.48395696149425	0.739237535887472	0.654670438120067	0.512679962329315	0.556623959100399
+TR2182|c3_g2_i6	wt_37	wt_ph8	2.76248771922916	1.94482465855284	2.353656188891	0.516404389322083	1.10366040723297	0.467901526536393	0.63985501178297	0.675402512437579
+TR3788|c0_g1_i1	wt_37	wt_ph8	23.7579432209456	26.0024682525169	24.8802057367313	-0.125340757750783	0.352879389384874	-0.355194328490741	0.722444013290729	0.741969527163451
+TR939|c0_g1_i1	wt_37	wt_ph8	103.002135647151	102.820214322362	102.911174984756	0.000973457550309434	0.195891269167835	0.00496937691222674	0.996035027203904	0.996035027203904
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,7 @@
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR4277|c0_g1_i1	wt_37	wt_ph8	4705.34614971641	162.902721493704	2434.12443560506	4.84804012036106	0.130783542648097	37.0691909868646	8.81406568413535e-301	3.34934495997143e-299	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4761|c0_g1_i1	wt_37	wt_ph8	2012.6141923276	384.620292965437	1198.61724264652	2.38432084623308	0.148099583891604	16.0994432501458	2.57410332221217e-58	2.44539815610156e-57	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR2107|c1_g1_i1	wt_37	wt_ph8	59.5986596731862	1.89840873462066	30.7485342039034	4.82151434610286	0.613172060454942	7.86323229164347	3.74345886500564e-15	1.29319488063831e-14	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR5055|c0_g2_i1	wt_37	wt_ph8	28.6665933385886	6.05959103586122	17.3630921872249	2.18372312866756	0.505600668447204	4.31906693354301	1.5669025864333e-05	3.30790546024808e-05	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
+TR127|c1_g1_i1	wt_37	wt_ph8	16.3791628279609	1.58772512712498	8.98344397754296	3.22742307122337	0.758365755070441	4.25576056097574	2.08339575851481e-05	4.16679151702962e-05	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR1894|c2_g1_i1	wt_37	wt_ph8	16.2826445742552	1.67571344127509	8.97917900776516	3.18830464179373	0.7590595028564	4.20033558607184	2.66519649541344e-05	5.06387334128554e-05	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,5 @@
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR131|c0_g1_i1	wt_37	wt_ph8	32.0461070493257	1436.30905989883	734.177583474076	-5.48335951236111	0.197548955320184	-27.7569653733364	1.43583336471356e-169	2.72808339295576e-168	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR3091|c0_g1_i1	wt_37	wt_ph8	20.4914097091341	321.651020117047	171.071214913091	-3.97084930318667	0.245881056057371	-16.1494722971263	1.14537343838751e-58	1.45080635529084e-57	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR5075|c0_g1_i1	wt_37	wt_ph8	19.3833722195684	136.98672801182	78.1850501156942	-2.80247674171473	0.269715041166808	-10.3905096637956	2.73885623424733e-25	2.08153073802797e-24	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
+TR2779|c0_g1_i1	wt_37	wt_ph8	191.51955185349	1058.15934185376	624.839446853626	-2.45909834872711	0.247058756007882	-9.95349603658112	2.43476309780354e-23	1.54201662860891e-22	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,39 +1,39 @@
-logFC	logCPM	PValue	FDR
-TR131|c0_g1_i1	5.83867709149149	16.0447742820606	3.67956255674e-64	1.3982337715612e-62
-TR3091|c0_g1_i1	4.35104356420213	13.9337836495047	7.47918124727105e-59	1.4210444369815e-57
-TR4277|c0_g1_i1	-4.51249642920563	17.4585638169146	1.30305812944242e-53	1.65054029729373e-52
-TR5075|c0_g1_i1	3.18286810352713	12.8084040893566	8.25600206225396e-24	7.84320195914126e-23
-TR2107|c1_g1_i1	-4.48477961203985	11.2510359028096	1.80754966502889e-22	1.37373774542196e-21
-TR2779|c0_g1_i1	2.75442228103487	15.7797198210508	8.23352696880425e-15	5.21456708024269e-14
-TR1891|c0_g1_i1	1.85607282303223	14.4424161372431	4.82341414399837e-12	2.61842482102769e-11
-TR4761|c0_g1_i1	-2.05815692521639	16.4916266891202	6.53530817860542e-12	3.10427138483757e-11
-TR1479|c0_g1_i1	1.43256512308186	14.3771181295432	1.13197856555697e-09	4.77946505457389e-09
-TR2122|c0_g2_i2	1.63807722824331	14.4300672231344	2.54380104198531e-09	9.66644395954419e-09
-TR24|c0_g1_i1	1.56169455062581	13.613754007054	1.01137959952142e-08	3.49385679834671e-08
-TR2487|c0_g1_i1	1.52157644373511	15.8810635663776	2.37540305111961e-07	7.52210966187877e-07
-TR4084|c0_g1_i1	0.991060679215133	13.5661427311877	4.21767858359174e-07	1.23285989366528e-06
-TR1678|c0_g1_i1	3.62458577193226	9.02581543875671	1.43837087677047e-05	3.90414952266271e-05
-TR127|c1_g1_i1	-2.90111481011278	9.73961125813442	2.21824302925283e-05	5.61954900744051e-05
-TR1894|c2_g1_i1	-2.85359093751189	9.70265145133598	3.82707393478771e-05	9.08930059512081e-05
-TR5055|c0_g2_i1	-1.8545312748531	10.5508309427169	0.000561739096452478	0.0012556520979526
-TR2090|c0_g1_i1	5.85461418677349	8.72713197001274	0.000625444406369261	0.00132038263566844
-TR4859|c0_g1_i1	-2.31469487039419	9.12085022188999	0.00236706272759891	0.00473412545519782
-TR1492|c0_g1_i2	-0.847097868783511	16.8160271449712	0.00265383515294934	0.00504228679060374
-TR3638|c0_g1_i1	-0.812580107843708	15.3469752226999	0.00403607816905259	0.00730337954399992
-TR3807|c0_g1_i1	-2.92018331334326	8.37863764275674	0.0119536481076316	0.0206472103677272
-TR1449|c0_g1_i1	-0.576747771663695	13.7363876885022	0.0130185393324759	0.0215088910710471
-TR1982|c2_g1_i1	1.11743546508384	9.86122459596308	0.024471659211255	0.0382656346855499
-TR2672|c0_g1_i1	-1.09825528852042	10.4080374441724	0.025174759661546	0.0382656346855499
-TR3249|c0_g1_i1	2.00776956676821	8.66772655901099	0.0275363688345113	0.0402454621427472
-TR5212|c0_g1_i1	0.582012857882519	12.8600915149255	0.0318599127004672	0.0448398771339909
-TR4163|c0_g1_i1	-0.585935901552979	14.6858409740027	0.0333717283041774	0.0452902026985264
-TR2844|c0_g1_i1	0.484938504762758	14.0537413817093	0.0410237194953782	0.0537552186491163
-TR1859|c3_g1_i1	2.64648031785777	8.0811923384908	0.0677782555815868	0.0858524570700099
-TR2278|c0_g1_i1	-0.462893051132405	15.2205527935145	0.0990317248813937	0.121393727273966
-TR3854|c0_g1_i1	0.45233145936844	17.3656486469949	0.115995274036176	0.13774438791796
-TR3788|c0_g1_i1	0.512277745155381	11.1125640718165	0.129462204245195	0.149077689736891
-TR939|c0_g1_i1	0.343195417039388	13.0829763503018	0.196684960972624	0.219824368145874
-TR1837|c2_g1_i1	2.21076601464763	7.9226544260522	0.248563909756302	0.269869387735413
-TR1122|c0_g1_i1	-0.860567840252952	7.98418712954456	0.72405804618472	0.764283493194982
-TR2011|c5_g1_i1	-0.075980865610854	9.27931055760989	0.901508002533997	0.925873083683564
-TR2182|c3_g2_i6	-0.147124070779728	8.45393312498213	1	1
+sampleA	sampleB	logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	wt_37	wt_ph8	-5.83867709149149	16.0447742820606	3.67956255674e-64	1.3982337715612e-62
+TR3091|c0_g1_i1	wt_37	wt_ph8	-4.35104356420213	13.9337836495047	7.47918124727105e-59	1.4210444369815e-57
+TR4277|c0_g1_i1	wt_37	wt_ph8	4.51249642920563	17.4585638169146	1.30305812944242e-53	1.65054029729373e-52
+TR5075|c0_g1_i1	wt_37	wt_ph8	-3.18286810352713	12.8084040893566	8.25600206225396e-24	7.84320195914126e-23
+TR2107|c1_g1_i1	wt_37	wt_ph8	4.48477961203985	11.2510359028096	1.80754966502889e-22	1.37373774542196e-21
+TR2779|c0_g1_i1	wt_37	wt_ph8	-2.75442228103487	15.7797198210508	8.23352696880425e-15	5.21456708024269e-14
+TR1891|c0_g1_i1	wt_37	wt_ph8	-1.85607282303223	14.4424161372431	4.82341414399837e-12	2.61842482102769e-11
+TR4761|c0_g1_i1	wt_37	wt_ph8	2.05815692521639	16.4916266891202	6.53530817860542e-12	3.10427138483757e-11
+TR1479|c0_g1_i1	wt_37	wt_ph8	-1.43256512308186	14.3771181295432	1.13197856555697e-09	4.77946505457389e-09
+TR2122|c0_g2_i2	wt_37	wt_ph8	-1.63807722824331	14.4300672231344	2.54380104198531e-09	9.66644395954419e-09
+TR24|c0_g1_i1	wt_37	wt_ph8	-1.56169455062581	13.613754007054	1.01137959952142e-08	3.49385679834671e-08
+TR2487|c0_g1_i1	wt_37	wt_ph8	-1.52157644373511	15.8810635663776	2.37540305111961e-07	7.52210966187877e-07
+TR4084|c0_g1_i1	wt_37	wt_ph8	-0.991060679215133	13.5661427311877	4.21767858359174e-07	1.23285989366528e-06
+TR1678|c0_g1_i1	wt_37	wt_ph8	-3.62458577193226	9.02581543875671	1.43837087677047e-05	3.90414952266271e-05
+TR127|c1_g1_i1	wt_37	wt_ph8	2.90111481011278	9.73961125813442	2.21824302925283e-05	5.61954900744051e-05
+TR1894|c2_g1_i1	wt_37	wt_ph8	2.85359093751189	9.70265145133598	3.82707393478771e-05	9.08930059512081e-05
+TR5055|c0_g2_i1	wt_37	wt_ph8	1.8545312748531	10.5508309427169	0.000561739096452478	0.0012556520979526
+TR2090|c0_g1_i1	wt_37	wt_ph8	-5.85461418677349	8.72713197001274	0.000625444406369261	0.00132038263566844
+TR4859|c0_g1_i1	wt_37	wt_ph8	2.31469487039419	9.12085022188999	0.00236706272759891	0.00473412545519782
+TR1492|c0_g1_i2	wt_37	wt_ph8	0.847097868783511	16.8160271449712	0.00265383515294934	0.00504228679060374
+TR3638|c0_g1_i1	wt_37	wt_ph8	0.812580107843708	15.3469752226999	0.00403607816905259	0.00730337954399992
+TR3807|c0_g1_i1	wt_37	wt_ph8	2.92018331334326	8.37863764275674	0.0119536481076316	0.0206472103677272
+TR1449|c0_g1_i1	wt_37	wt_ph8	0.576747771663695	13.7363876885022	0.0130185393324759	0.0215088910710471
+TR1982|c2_g1_i1	wt_37	wt_ph8	-1.11743546508384	9.86122459596308	0.024471659211255	0.0382656346855499
+TR2672|c0_g1_i1	wt_37	wt_ph8	1.09825528852042	10.4080374441724	0.025174759661546	0.0382656346855499
+TR3249|c0_g1_i1	wt_37	wt_ph8	-2.00776956676821	8.66772655901099	0.0275363688345113	0.0402454621427472
+TR5212|c0_g1_i1	wt_37	wt_ph8	-0.582012857882519	12.8600915149255	0.0318599127004672	0.0448398771339909
+TR4163|c0_g1_i1	wt_37	wt_ph8	0.585935901552979	14.6858409740027	0.0333717283041774	0.0452902026985264
+TR2844|c0_g1_i1	wt_37	wt_ph8	-0.484938504762758	14.0537413817093	0.0410237194953782	0.0537552186491163
+TR1859|c3_g1_i1	wt_37	wt_ph8	-2.64648031785777	8.0811923384908	0.0677782555815868	0.0858524570700099
+TR2278|c0_g1_i1	wt_37	wt_ph8	0.462893051132405	15.2205527935145	0.0990317248813937	0.121393727273966
+TR3854|c0_g1_i1	wt_37	wt_ph8	-0.45233145936844	17.3656486469949	0.115995274036176	0.13774438791796
+TR3788|c0_g1_i1	wt_37	wt_ph8	-0.512277745155381	11.1125640718165	0.129462204245195	0.149077689736891
+TR939|c0_g1_i1	wt_37	wt_ph8	-0.343195417039388	13.0829763503018	0.196684960972624	0.219824368145874
+TR1837|c2_g1_i1	wt_37	wt_ph8	-2.21076601464763	7.9226544260522	0.248563909756302	0.269869387735413
+TR1122|c0_g1_i1	wt_37	wt_ph8	0.860567840252952	7.98418712954456	0.72405804618472	0.764283493194982
+TR2011|c5_g1_i1	wt_37	wt_ph8	0.075980865610854	9.27931055760989	0.901508002533997	0.925873083683564
+TR2182|c3_g2_i6	wt_37	wt_ph8	0.147124070779728	8.45393312498213	1	1
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,39 +1,39 @@
-logFC	logCPM	PValue	FDR
-TR131|c0_g1_i1	5.89108692370307	16.0946870940125	4.52958285205525e-36	1.721241483781e-34
-TR4277|c0_g1_i1	-4.47812345668175	17.3786096664403	1.7008141018303e-32	3.23154679347758e-31
-TR3091|c0_g1_i1	4.37454375877296	13.9751350003907	7.58044859691792e-23	9.60190155609603e-22
-TR2779|c0_g1_i1	2.89398117484377	15.8061264352363	3.97828335136821e-18	3.7793691837998e-17
-TR5075|c0_g1_i1	3.21512246000432	12.8334153580766	2.0588784190888e-14	1.56474759850749e-13
-TR2107|c1_g1_i1	-4.32040270723487	11.0762608486921	9.69490500265428e-11	6.14010650168104e-10
-TR4761|c0_g1_i1	-2.00464775189483	16.4172477083723	2.27235196662378e-10	1.23356249616719e-09
-TR1891|c0_g1_i1	1.89490003648365	14.4620196202787	1.18363400337593e-09	5.62226151603565e-09
-TR2122|c0_g2_i2	1.68823123696301	14.4430864744705	3.40183177422869e-08	1.436328971341e-07
-TR24|c0_g1_i1	1.665273448047	13.6146325155501	1.25297628243395e-07	4.76130987324901e-07
-TR2487|c0_g1_i1	1.57111929409713	15.8914511338271	3.01913153313087e-07	1.04297271144521e-06
-TR1479|c0_g1_i1	1.45195340320994	14.3929474544484	1.34694977997748e-06	4.2653409699287e-06
-TR1678|c0_g1_i1	3.32711159096413	8.62991286220581	4.44668660347576e-05	0.000129980069947753
-TR127|c1_g1_i1	-2.68488776770857	9.36026180000128	0.000136507461427459	0.00037052025244596
-TR1894|c2_g1_i1	-2.65840371977461	9.30640094015976	0.000158988679158599	0.000402771320535117
-TR2090|c0_g1_i1	3.12073361486577	8.21515298661506	0.000414922023762837	0.000985439806436737
-TR5055|c0_g2_i1	-1.75449782198233	10.3047459168783	0.000987360143376457	0.0020844269693503
-TR4084|c0_g1_i1	0.990738086664283	13.5812840323914	0.000929878324478984	0.00207855154883538
-TR4859|c0_g1_i1	-2.03844841522755	8.5557148387818	0.00574511253124233	0.0114902250624847
-TR3807|c0_g1_i1	-2.27805436961797	7.32408068149202	0.00831980659467625	0.0150548881236999
-TR1859|c3_g1_i1	2.08358066039446	6.92308482511994	0.0216139227266133	0.0357099592874481
-TR1492|c0_g1_i2	-0.80292474159496	16.7717103141256	0.00797659176853916	0.0150548881236999
-TR3638|c0_g1_i1	-0.765536214533451	15.2959378061905	0.00929698340782949	0.0160584258862509
-TR2672|c0_g1_i1	-1.15555384827173	10.1973122527932	0.0235572978271919	0.0372990548930539
-TR3249|c0_g1_i1	1.48866796495104	8.06119288435276	0.0588654345124954	0.0794847966327657
-TR1982|c2_g1_i1	1.06368641289493	9.64628067316551	0.0510418091524593	0.0745995672228252
-TR1837|c2_g1_i1	1.43890969571076	6.48444225997254	0.130037630852572	0.154419686637429
-TR5212|c0_g1_i1	0.63168831011067	12.8380836623566	0.0456316928604782	0.0693601731479268
-TR4163|c0_g1_i1	-0.545743678134199	14.6411189904126	0.0582697662607788	0.0794847966327657
-TR1449|c0_g1_i1	-0.549932747054717	13.6939664483469	0.0606594500618475	0.0794847966327657
-TR2844|c0_g1_i1	0.508967050135572	14.0451022220879	0.0750763100520493	0.0950966593992624
-TR3854|c0_g1_i1	0.504473372285636	17.3527799714624	0.0956174473541405	0.117208483853463
-TR1122|c0_g1_i1	-0.501746583160273	6.50836597017328	0.595453777887275	0.628534543325457
-TR3788|c0_g1_i1	0.524753873079964	11.0311382344715	0.215975804877357	0.234488016723988
-TR2278|c0_g1_i1	-0.424377145183038	15.1829447141358	0.145500439954072	0.167545961159234
-TR2182|c3_g2_i6	0.0429471548350905	7.57134083040984	0.956400717774849	0.956400717774849
-TR939|c0_g1_i1	0.398499350568058	13.0523653134109	0.192129988432482	0.214733516483362
-TR2011|c5_g1_i1	0.0410416962762211	8.85697121679121	0.9477445647389	0.956400717774849
+sampleA	sampleB	logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	wt_37	wt_ph8	-5.89108692370307	16.0946870940125	5.83734002581789e-38	2.2181892098108e-36
+TR4277|c0_g1_i1	wt_37	wt_ph8	4.47812345668175	17.3786096664403	2.84916418820701e-34	5.41341195759331e-33
+TR3091|c0_g1_i1	wt_37	wt_ph8	-4.37454375877296	13.9751350003907	3.03684158911717e-24	3.84666601288175e-23
+TR2779|c0_g1_i1	wt_37	wt_ph8	-2.89398117484377	15.8061264352363	2.71183962208552e-19	2.57624764098124e-18
+TR5075|c0_g1_i1	wt_37	wt_ph8	-3.21512246000432	12.8334153580766	2.25968184332879e-15	1.71735820092988e-14
+TR2107|c1_g1_i1	wt_37	wt_ph8	4.32040270723487	11.0762608486921	1.80270537224079e-11	1.14171340241917e-10
+TR4761|c0_g1_i1	wt_37	wt_ph8	2.00464775189483	16.4172477083723	4.47039820077749e-11	2.42678759470778e-10
+TR1891|c0_g1_i1	wt_37	wt_ph8	-1.89490003648365	14.4620196202787	2.60196088184267e-10	1.23593141887527e-09
+TR2122|c0_g2_i2	wt_37	wt_ph8	-1.68823123696301	14.4430864744705	9.44150971333403e-09	3.98641521229659e-08
+TR24|c0_g1_i1	wt_37	wt_ph8	-1.665273448047	13.6146325155501	3.81691570216026e-08	1.4504279668209e-07
+TR2487|c0_g1_i1	wt_37	wt_ph8	-1.57111929409713	15.8914511338271	9.80135417366341e-08	3.3859223509019e-07
+TR1479|c0_g1_i1	wt_37	wt_ph8	-1.45195340320994	14.3929474544484	4.87972014978913e-07	1.54524471409989e-06
+TR1678|c0_g1_i1	wt_37	wt_ph8	-3.32711159096413	8.62991286220581	2.09660385386406e-05	6.12853434206418e-05
+TR127|c1_g1_i1	wt_37	wt_ph8	2.68488776770857	9.36026180000128	7.01712501052362e-05	0.000190464821714212
+TR1894|c2_g1_i1	wt_37	wt_ph8	2.65840371977461	9.30640094015976	8.26981533784737e-05	0.0002095019885588
+TR2090|c0_g1_i1	wt_37	wt_ph8	-3.12073361486577	8.21515298661506	0.000232532921389064	0.000552265688299028
+TR5055|c0_g2_i1	wt_37	wt_ph8	1.75449782198233	10.3047459168783	0.000592147419555538	0.00125008899683947
+TR4084|c0_g1_i1	wt_37	wt_ph8	-0.990738086664283	13.5812840323914	0.000555059638311732	0.00124072154446152
+TR4859|c0_g1_i1	wt_37	wt_ph8	2.03844841522755	8.5557148387818	0.00395651243262557	0.00791302486525114
+TR3807|c0_g1_i1	wt_37	wt_ph8	2.27805436961797	7.32408068149202	0.00589866928719914	0.0106737825196937
+TR1492|c0_g1_i2	wt_37	wt_ph8	0.80292474159496	16.7717103141256	0.00563666782754467	0.0106737825196937
+TR1859|c3_g1_i1	wt_37	wt_ph8	-2.08358066039446	6.92308482511994	0.0165122223690091	0.0272810630444498
+TR3638|c0_g1_i1	wt_37	wt_ph8	0.765536214533451	15.2959378061905	0.00664915219564581	0.0114848992470246
+TR2672|c0_g1_i1	wt_37	wt_ph8	1.15555384827173	10.1973122527932	0.0181178874953213	0.0286866552009254
+TR3249|c0_g1_i1	wt_37	wt_ph8	-1.48866796495104	8.06119288435276	0.0485882100928285	0.065758173656721
+TR1982|c2_g1_i1	wt_37	wt_ph8	-1.06368641289493	9.64628067316551	0.0416733207176468	0.0609071610488684
+TR1837|c2_g1_i1	wt_37	wt_ph8	-1.43890969571076	6.48444225997254	0.11393330230991	0.135295796493019
+TR5212|c0_g1_i1	wt_37	wt_ph8	-0.63168831011067	12.8380836623566	0.0369371606978983	0.0561444842608054
+TR4163|c0_g1_i1	wt_37	wt_ph8	0.545743678134199	14.6411189904126	0.0480591953597162	0.065758173656721
+TR1449|c0_g1_i1	wt_37	wt_ph8	0.549932747054717	13.6939664483469	0.0501838693696029	0.065758173656721
+TR2844|c0_g1_i1	wt_37	wt_ph8	-0.508967050135572	14.0451022220879	0.0631262591502691	0.0799599282570075
+TR3854|c0_g1_i1	wt_37	wt_ph8	-0.504473372285636	17.3527799714624	0.0818779321593283	0.100366497485628
+TR1122|c0_g1_i1	wt_37	wt_ph8	0.501746583160273	6.50836597017328	0.579206371120405	0.611384502849316
+TR3788|c0_g1_i1	wt_37	wt_ph8	-0.524753873079964	11.0311382344715	0.196342217213272	0.213171550117267
+TR2278|c0_g1_i1	wt_37	wt_ph8	0.424377145183038	15.1829447141358	0.128541258915261	0.148017207235755
+TR2182|c3_g2_i6	wt_37	wt_ph8	-0.0429471548350905	7.57134083040984	0.954463369529891	0.954463369529891
+TR939|c0_g1_i1	wt_37	wt_ph8	-0.398499350568058	13.0523653134109	0.173205070507278	0.193582137625782
+TR2011|c5_g1_i1	wt_37	wt_ph8	-0.0410416962762211	8.85697121679121	0.94542366790428	0.954463369529891
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,40 +1,40 @@
 sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
-TR2779|c0_g1_i1	wt_GSNO	wt_ph8	195.849684476753	966.924129135581	581.386906806167	-2.26327524632747	0.139880929176731	-16.1800129556472	6.97797522934818e-59	2.3027318256849e-57
-TR1891|c0_g1_i1	wt_GSNO	wt_ph8	128.246229498835	343.028289972482	235.637259735659	-1.40437008666625	0.103208263182426	-13.6071477550587	3.63141533276091e-42	5.99183529905551e-41
-TR4761|c0_g1_i1	wt_GSNO	wt_ph8	184.029205648389	351.782300021135	267.905752834762	-0.934295661860181	0.0925945355062913	-10.0901814210915	6.10565695161207e-24	6.71622264677328e-23
-TR24|c0_g1_i1	wt_GSNO	wt_ph8	39.3724575919554	183.288101009647	111.330279300801	-2.12198385961523	0.229366226812664	-9.25150964508988	2.21344016014191e-20	1.82608813211707e-19
-TR3638|c0_g1_i1	wt_GSNO	wt_ph8	174.266398355818	297.555274221606	235.910836288712	-0.755625651268871	0.0961172743232099	-7.86149687024996	3.79569918101421e-15	2.50516145946938e-14
-TR2122|c0_g2_i2	wt_GSNO	wt_ph8	190.673533226329	328.707071692642	259.690302459485	-0.781951344246178	0.102125767694546	-7.65674875105918	1.90699193392882e-14	1.04884556366085e-13
-TR2278|c0_g1_i1	wt_GSNO	wt_ph8	426.804298570637	315.99710709695	371.400702833793	0.428907012124225	0.105320470989525	4.07239929801383	4.65313200258197e-05	0.000219361937264579
-TR4084|c0_g1_i1	wt_GSNO	wt_ph8	115.544575735664	157.970364768418	136.757470252041	-0.434913653199297	0.157209464946713	-2.76645972522529	0.00566685842046991	0.0233757909844384
-TR3788|c0_g1_i1	wt_GSNO	wt_ph8	128.115824993653	24.010679388938	76.0632521912957	1.36551096405932	0.534260069919225	2.55589186043003	0.0105916029199559	0.0388358773731717
-TR1492|c0_g1_i2	wt_GSNO	wt_ph8	1368.89238848897	813.514514376559	1091.20345143276	0.692062260203308	0.290167592747528	2.38504325603812	0.0170771132686324	0.0563544737864868
-TR1678|c0_g1_i1	wt_GSNO	wt_ph8	0.695005959508731	7.10082184137838	3.89791390044355	-1.19229893380239	0.533516728634619	-2.23479203145837	0.0254310052417055	0.0762930157251164
-TR5075|c0_g1_i1	wt_GSNO	wt_ph8	8.81552188359314	126.23137395943	67.5234479215117	-1.10768013972448	0.513345367512952	-2.15776786900981	0.0309458842036983	0.0851011815601704
-TR1479|c0_g1_i1	wt_GSNO	wt_ph8	353.92669362375	305.546165789569	329.736429706659	0.210154850632672	0.101920088147959	2.06195711219939	0.0392118193266939	0.0995376952139152
-TR1859|c3_g1_i1	wt_GSNO	wt_ph8	0	2.05957798928713	1.02978899464357	-1.01742987508067	0.500302018271162	-2.03363136250477	0.0419887772494581	1
-TR2844|c0_g1_i1	wt_GSNO	wt_ph8	220.566338218013	194.214843050373	207.390590634193	0.185176880395552	0.100284765132021	1.84651058564851	0.0648181037840442	0.152785530348104
-TR2107|c1_g1_i1	wt_GSNO	wt_ph8	7.08292121571621	1.78415791317121	4.43353956444371	0.951944042839851	0.540599552522162	1.76090423752399	0.0782546125949942	0.170760316089935
-TR4669|c0_g2_i1	wt_GSNO	wt_ph8	165.630009730314	0	82.8150048651569	0.762969565911357	0.439826422982926	1.73470607049221	0.0827928805284532	0.170760316089935
-TR2672|c0_g1_i1	wt_GSNO	wt_ph8	2.07518941673641	7.44710458698621	4.76114700186131	-0.686459125319668	0.52860452101472	-1.29862514986048	0.194072602638997	0.376729169828641
-TR4859|c0_g1_i1	wt_GSNO	wt_ph8	3.10763825129944	1.1806627783491	2.14415051482427	0.593225714064679	0.537217960853533	1.10425517628294	0.269482460872864	0.494051178266917
-TR3091|c0_g1_i1	wt_GSNO	wt_ph8	312.47018793986	293.531643106953	303.000915523406	0.0878939148373507	0.0878811164283744	1.00014563320878	0.317240035048796	0.536180698490786
-TR4163|c0_g1_i1	wt_GSNO	wt_ph8	221.469120691076	207.118822998308	214.293971844692	0.0959413488001967	0.0974696330347526	0.984320406397642	0.324957999085325	0.536180698490786
-TR1894|c2_g1_i1	wt_GSNO	wt_ph8	2.85762748931802	1.47338219762144	2.16550484346973	0.431530486406946	0.537372709941065	0.803037590900872	0.421953007665329	0.663069012045517
-TR3249|c0_g1_i1	wt_GSNO	wt_ph8	2.06512931203634	4.15451161800812	3.10982046502223	-0.38612563978518	0.523142120053183	-0.738089373774619	0.460460140618999	0.675718500003336
-TR5212|c0_g1_i1	wt_GSNO	wt_ph8	102.736339436612	86.4452993262187	94.5908193814151	0.226915890105892	0.314756340859895	0.720925556212693	0.470955318184143	0.675718500003336
-TR1122|c0_g1_i1	wt_GSNO	wt_ph8	1.29006258579706	0.5946183773076	0.942340481552333	0.279366026492593	0.486443515520964	0.57430311552905	0.565762701275693	1
-TR2011|c5_g1_i1	wt_GSNO	wt_ph8	7.597917075274	4.42090354598533	6.00941031062966	0.293830308686626	0.525066976727929	0.559605386950241	0.575748629670957	0.791654365797565
-TR1837|c2_g1_i1	wt_GSNO	wt_ph8	2.16507864525674	1.46465683073113	1.81486773799393	0.232644077202222	0.530765383353658	0.438318105322267	0.661155703054792	1
-TR1982|c2_g1_i1	wt_GSNO	wt_ph8	5.5352448786851	10.687042573374	8.11114372602957	-0.163617497783336	0.41190705551325	-0.397219459082736	0.691205633846634	0.874699343226649
-TR1449|c0_g1_i1	wt_GSNO	wt_ph8	98.9943307118646	106.843279101242	102.918804906553	-0.100378154615576	0.259464578599584	-0.38686650469729	0.69885503944156	0.874699343226649
-TR2182|c3_g2_i6	wt_GSNO	wt_ph8	1.29006258579706	1.76655578876639	1.52830918728173	-0.199699696686908	0.518464312092113	-0.385175395932417	0.700107470922461	1
-TR4277|c0_g1_i1	wt_GSNO	wt_ph8	153.969096204861	149.159426886469	151.564261545665	0.0459499001744168	0.126145529370448	0.364261027748966	0.715663099003622	0.874699343226649
-TR3854|c0_g1_i1	wt_GSNO	wt_ph8	2260.55060252051	1927.46472630351	2094.00766441201	0.149461409336011	0.515737174792397	0.289801504799756	0.771968096584582	0.909819542403257
-TR127|c1_g1_i1	wt_GSNO	wt_ph8	1.20754470361908	1.49113571265046	1.34934020813477	-0.140499936513031	0.525109891787989	-0.267562921038549	0.789035775295455	1
-TR2090|c0_g1_i1	wt_GSNO	wt_ph8	9.46045896251181	5.6546754787973	7.55756722065455	0.0558182109444541	0.287850208274631	0.193914089133468	0.846243151562143	0.956832805790417
-TR3807|c0_g1_i1	wt_GSNO	wt_ph8	0.347502979754365	0.292870809896544	0.320186894825454	0.0816135421729034	0.465942705668376	0.175157892118586	0.860955569985101	1
-TR131|c0_g1_i1	wt_GSNO	wt_ph8	1275.67603302799	1312.2934796972	1293.9847563626	-0.035805337908038	0.355352253126282	-0.100760126305753	0.919740880292126	0.956832805790417
-TR5055|c0_g2_i1	wt_GSNO	wt_ph8	5.17791343714095	5.60171771495863	5.38981557604979	-0.0489219520111245	0.535247232645477	-0.091400663146498	0.927174234841818	0.956832805790417
-TR939|c0_g1_i1	wt_GSNO	wt_ph8	92.2508462008296	94.0990807885678	93.1749634946987	-0.0260132924520656	0.31360944301959	-0.0829480522065804	0.933892845523313	0.956832805790417
-TR2487|c0_g1_i1	wt_GSNO	wt_ph8	875.181494043204	882.631049341941	878.906271692572	-0.0117684251443531	0.217416529127567	-0.0541284749212796	0.956832805790417	0.956832805790417
+TR2779|c0_g1_i1	wt_GSNO	wt_ph8	195.849684476753	966.924129135581	581.386906806167	-2.30255444666643	0.142496869452374	-16.1586318037394	9.87286349195067e-59	3.65295949202175e-57
+TR1891|c0_g1_i1	wt_GSNO	wt_ph8	128.246229498835	343.028289972482	235.637259735659	-1.41742353970608	0.104322254921725	-13.5869718380762	4.7847024102546e-42	8.85169945897101e-41
+TR4761|c0_g1_i1	wt_GSNO	wt_ph8	184.029205648389	351.782300021135	267.905752834762	-0.941259207260894	0.0933372308442124	-10.0844989587481	6.46943903995441e-24	7.97897481594377e-23
+TR24|c0_g1_i1	wt_GSNO	wt_ph8	39.3724575919554	183.288101009647	111.330279300801	-2.22846767043702	0.242443002218043	-9.19171784728532	3.8661704482204e-20	3.57620766460387e-19
+TR3638|c0_g1_i1	wt_GSNO	wt_ph8	174.266398355818	297.555274221606	235.910836288712	-0.761689698593786	0.0969314803260852	-7.85802193499368	3.90246977317854e-15	2.88782763215212e-14
+TR2122|c0_g2_i2	wt_GSNO	wt_ph8	190.673533226329	328.707071692642	259.690302459485	-0.789061688115738	0.103094089827306	-7.65380139091878	1.95123561208803e-14	1.20326196078762e-13
+TR4669|c0_g2_i1	wt_GSNO	wt_ph8	165.630009730314	0	82.8150048651569	9.98638581786287	2.4059110197361	4.15077105343582	3.31357095211564e-05	0.000175145893183255
+TR2278|c0_g1_i1	wt_GSNO	wt_ph8	426.804298570637	315.99710709695	371.400702833793	0.433055347501052	0.106340324733669	4.07235306630524	4.65405596936774e-05	0.000215250088583258
+TR4084|c0_g1_i1	wt_GSNO	wt_ph8	115.544575735664	157.970364768418	136.757470252041	-0.444508945050626	0.160721197310781	-2.76571449496544	0.00567982380522758	0.0233503867548245
+TR3788|c0_g1_i1	wt_GSNO	wt_ph8	128.115824993653	24.010679388938	76.0632521912957	2.41599826196159	0.930388620648254	2.59676248004649	0.00941069736444863	0.0348195802484599
+TR5075|c0_g1_i1	wt_GSNO	wt_ph8	8.81552188359314	126.23137395943	67.5234479215117	-3.83892667969009	1.51640337447055	-2.53159993199728	0.011354345783228	0.0381918903617669
+TR1492|c0_g1_i2	wt_GSNO	wt_ph8	1368.89238848897	813.514514376559	1091.20345143276	0.750717599362045	0.314762309207928	2.38503015577424	0.0170777214032423	0.0526563076599971
+TR1678|c0_g1_i1	wt_GSNO	wt_ph8	0.695005959508731	7.10082184137838	3.89791390044355	-3.29023865439926	1.5074251817588	-2.18268786684349	0.0290588040465388	0.0827058269016874
+TR1479|c0_g1_i1	wt_GSNO	wt_ph8	353.92669362375	305.546165789569	329.736429706659	0.212056310257658	0.102841330599285	2.0619755600394	0.0392100628615421	0.0987833713777749
+TR1859|c3_g1_i1	wt_GSNO	wt_ph8	0	2.05957798928713	1.02978899464357	-3.32897459707672	1.62131131542189	-2.05326057087961	0.0400473127207196	0.0987833713777749
+TR2844|c0_g1_i1	wt_GSNO	wt_ph8	220.566338218013	194.214843050373	207.390590634193	0.186796872895526	0.101161116569868	1.84652838194517	0.0648155222548659	0.149885895214377
+TR2107|c1_g1_i1	wt_GSNO	wt_ph8	7.08292121571621	1.78415791317121	4.43353956444371	1.99039306371489	1.13345482120555	1.75604093473959	0.0790814192380851	0.172118383047597
+TR2672|c0_g1_i1	wt_GSNO	wt_ph8	2.07518941673641	7.44710458698621	4.76114700186131	-1.80710364026684	1.37881760417113	-1.31061834052603	0.189986739707575	0.390528298287793
+TR4859|c0_g1_i1	wt_GSNO	wt_ph8	3.10763825129944	1.1806627783491	2.14415051482427	1.36600125700608	1.2414304168313	1.10034460126467	0.271182006077654	0.528091274993326
+TR3091|c0_g1_i1	wt_GSNO	wt_ph8	312.47018793986	293.531643106953	303.000915523406	0.0884824617062972	0.0884687505769758	1.00015498273946	0.317235511103454	0.572534846407878
+TR4163|c0_g1_i1	wt_GSNO	wt_ph8	221.469120691076	207.118822998308	214.293971844692	0.0967338751775769	0.0982736079923787	0.984332183927538	0.32495221012339	0.572534846407878
+TR1894|c2_g1_i1	wt_GSNO	wt_ph8	2.85762748931802	1.47338219762144	2.16550484346973	0.974874448083219	1.21963227734233	0.799318340612911	0.424105846774723	0.713268924121126
+TR3249|c0_g1_i1	wt_GSNO	wt_ph8	2.06512931203634	4.15451161800812	3.10982046502223	-1.06280923847799	1.42172379433194	-0.747549729923031	0.454731796166148	0.726065302514322
+TR5212|c0_g1_i1	wt_GSNO	wt_ph8	102.736339436612	86.4452993262187	94.5908193814151	0.250307109752951	0.347207101059694	0.720915871216346	0.470961277306587	0.726065302514322
+TR1122|c0_g1_i1	wt_GSNO	wt_ph8	1.29006258579706	0.5946183773076	0.942340481552333	1.01745920560278	1.75106315862361	0.581052259932493	0.56120523253296	1
+TR2011|c5_g1_i1	wt_GSNO	wt_ph8	7.597917075274	4.42090354598533	6.00941031062966	0.776221433822186	1.38068634268934	0.562199689981896	0.573979972628347	0.849490359489954
+TR1837|c2_g1_i1	wt_GSNO	wt_ph8	2.16507864525674	1.46465683073113	1.81486773799393	0.574055870722254	1.31330872914193	0.437106567545105	0.662034064585522	0.882648546299865
+TR1982|c2_g1_i1	wt_GSNO	wt_ph8	5.5352448786851	10.687042573374	8.11114372602957	-0.948745824078601	2.34310116245329	-0.404910312572778	0.685543437736556	0.882648546299865
+TR2182|c3_g2_i6	wt_GSNO	wt_ph8	1.29006258579706	1.76655578876639	1.52830918728173	-0.570835750385155	1.46441538912588	-0.389804528567464	0.69668109483689	0.882648546299865
+TR1449|c0_g1_i1	wt_GSNO	wt_ph8	98.9943307118646	106.843279101242	102.918804906553	-0.106933839690288	0.276431863357554	-0.386836156988073	0.69887750768045	0.882648546299865
+TR4277|c0_g1_i1	wt_GSNO	wt_ph8	153.969096204861	149.159426886469	151.564261545665	0.0465928591854992	0.127909639606222	0.364263861026723	0.715660983486377	0.882648546299865
+TR3854|c0_g1_i1	wt_GSNO	wt_ph8	2260.55060252051	1927.46472630351	2094.00766441201	0.229965172704227	0.793466242289153	0.289823511635197	0.771951259799022	0.910963182508483
+TR127|c1_g1_i1	wt_GSNO	wt_ph8	1.20754470361908	1.49113571265046	1.34934020813477	-0.373671738849606	1.38864714646401	-0.269090488394483	0.787860049737066	0.910963182508483
+TR2090|c0_g1_i1	wt_GSNO	wt_ph8	9.46045896251181	5.6546754787973	7.55756722065455	0.740040477295998	3.75055668025179	0.197314836272869	0.843581169905129	0.945833432923932
+TR3807|c0_g1_i1	wt_GSNO	wt_ph8	0.347502979754365	0.292870809896544	0.320186894825454	0.331202385322154	1.89086385045429	0.175159298350635	0.86095446505486	1
+TR131|c0_g1_i1	wt_GSNO	wt_ph8	1275.67603302799	1312.2934796972	1293.9847563626	-0.0408368749216097	0.405274721880973	-0.100763439506112	0.919738250126613	0.956831887096638
+TR5055|c0_g2_i1	wt_GSNO	wt_ph8	5.17791343714095	5.60171771495863	5.38981557604979	-0.113901914254779	1.2463123048955	-0.0913911495596841	0.927181793948424	0.956831887096638
+TR939|c0_g1_i1	wt_GSNO	wt_ph8	92.2508462008296	94.0990807885678	93.1749634946987	-0.0286723936076206	0.345661698999542	-0.0829492931690373	0.933891858779013	0.956831887096638
+TR2487|c0_g1_i1	wt_GSNO	wt_ph8	875.181494043204	882.631049341941	878.906271692572	-0.0122873741271452	0.226999049805604	-0.0541296280212089	0.956831887096638	0.956831887096638
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,1 @@
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,3 @@
+sampleA	sampleB	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR2779|c0_g1_i1	wt_GSNO	wt_ph8	195.849684476753	966.924129135581	581.386906806167	-2.26327524632747	0.139880929176731	-16.1800129556472	6.97797522934818e-59	2.3027318256849e-57	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR24|c0_g1_i1	wt_GSNO	wt_ph8	39.3724575919554	183.288101009647	111.330279300801	-2.12198385961523	0.229366226812664	-9.25150964508988	2.21344016014191e-20	1.82608813211707e-19	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,40 +1,40 @@
-logFC	logCPM	PValue	FDR
-TR2779|c0_g1_i1	2.23948335958727	15.9163308249372	1.20766376889896e-237	4.70988869870595e-236
-TR1492|c0_g1_i2	-0.807859120941235	16.8439348559211	2.37986391219743e-61	4.64073462878498e-60
-TR1891|c0_g1_i1	1.35697452203657	14.6311197032228	1.60645028176433e-35	2.08838536629363e-34
-TR4761|c0_g1_i1	0.880921757190946	14.8138260614735	1.59143301924913e-24	1.5516471937679e-23
-TR2122|c0_g2_i2	0.729785350305026	14.7699678361852	6.52776857951534e-13	5.09165949202196e-12
-TR3854|c0_g1_i1	-0.289859344737128	17.7786469452325	6.1302236270955e-12	3.98464535761207e-11
-TR3638|c0_g1_i1	0.702510801497461	14.6355179638282	5.62335492840333e-11	3.133012031539e-10
-TR2278|c0_g1_i1	-0.490901034745758	15.2921454021456	1.53296499052609e-09	7.47320432881468e-09
-TR24|c0_g1_i1	2.16007337608378	13.5636496776551	8.67157466173412e-09	3.75768235341812e-08
-TR5075|c0_g1_i1	3.7524485458028	12.8683202800317	5.50095216588421e-08	2.14537134469484e-07
-TR4669|c0_g2_i1	-10.4044948993067	13.1110475123695	1.35189372056785e-06	4.79307773655872e-06
-TR3788|c0_g1_i1	-2.47698512550917	13.0240883091698	1.80487840553907e-05	5.86585481800198e-05
-TR1479|c0_g1_i1	-0.272661827455658	15.1172528121102	0.000483095512098729	0.00144928653629619
-TR1678|c0_g1_i1	3.02812287247775	9.36059212330112	0.0074853976481696	0.0208521791627582
-TR2107|c1_g1_i1	-1.98032359155541	9.36544178725855	0.0305238827180189	0.0756824353198294
-TR2844|c0_g1_i1	-0.244755727600329	14.4560017424587	0.0310492042337762	0.0756824353198294
-TR1859|c3_g1_i1	4.12978123132011	8.37588761488442	0.0428877609330621	0.0983895691993777
-TR3091|c0_g1_i1	-0.148576217250104	14.9963238698071	0.0547318692708507	0.11858571675351
-TR2672|c0_g1_i1	1.64029381826409	9.53984158811941	0.100507062957769	0.206303971334369
-TR4163|c0_g1_i1	-0.156926020788278	14.5006265631178	0.113620071038851	0.22155913852576
-TR4859|c0_g1_i1	-1.3062724221166	8.73091245897321	0.181160758857669	0.3364414093071
-TR4084|c0_g1_i1	0.390578563212142	13.8603174460746	0.270419882900116	0.479380701504752
-TR1982|c2_g1_i1	0.866592651710305	10.0958159836705	0.312186869456376	0.515984430920105
-TR1894|c2_g1_i1	-0.989932992780787	8.78384403630691	0.317528880566218	0.515984430920105
-TR4277|c0_g1_i1	-0.107189584823599	14.0046148411409	0.347278576725125	0.541754579691195
-TR2487|c0_g1_i1	-0.0467513454249246	16.526653433485	0.376403968202147	0.560230359736405
-TR3249|c0_g1_i1	1.00369455926223	9.08504250192555	0.387851787509819	0.560230359736405
-TR5212|c0_g1_i1	-0.310409394484433	13.3365591825697	0.416163942507532	0.572783249883747
-TR2011|c5_g1_i1	-0.799376994792807	9.70509536731836	0.425915749913555	0.572783249883747
-TR1837|c2_g1_i1	-0.59484087321072	8.66193471010726	0.588495494688377	0.76504414309489
-TR2090|c0_g1_i1	-0.766971023107968	9.89421471118339	0.638322407555079	0.8030507707951
-TR131|c0_g1_i1	-0.0187996511046741	17.0827735361623	0.697507705031756	0.850087515507453
-TR1122|c0_g1_i1	-0.908051089281089	8.22928258978683	0.753364106379395	0.890339398448377
-TR1449|c0_g1_i1	0.0452741219590205	13.4583026590017	0.919111339143084	1
-TR939|c0_g1_i1	-0.0309689709592036	13.3146949564453	0.956245904999637	1
-TR5055|c0_g2_i1	0.0548476287872344	9.62768102188797	0.999999999999985	1
-TR2182|c3_g2_i6	0.517423422896207	8.5297276065799	1	1
-TR127|c1_g1_i1	0.299043611515333	8.4576897025083	1	1
-TR3807|c0_g1_i1	-0.266132577378544	7.94319410024963	1	1
+sampleA	sampleB	logFC	logCPM	PValue	FDR
+TR2779|c0_g1_i1	wt_GSNO	wt_ph8	-2.23948335958727	15.9163308249372	1.20766376889896e-237	4.70988869870595e-236
+TR1492|c0_g1_i2	wt_GSNO	wt_ph8	0.807859120941235	16.8439348559211	2.37986391219743e-61	4.64073462878498e-60
+TR1891|c0_g1_i1	wt_GSNO	wt_ph8	-1.35697452203657	14.6311197032228	1.60645028176433e-35	2.08838536629363e-34
+TR4761|c0_g1_i1	wt_GSNO	wt_ph8	-0.880921757190946	14.8138260614735	1.59143301924913e-24	1.5516471937679e-23
+TR2122|c0_g2_i2	wt_GSNO	wt_ph8	-0.729785350305026	14.7699678361852	6.52776857951534e-13	5.09165949202196e-12
+TR3854|c0_g1_i1	wt_GSNO	wt_ph8	0.289859344737128	17.7786469452325	6.1302236270955e-12	3.98464535761207e-11
+TR3638|c0_g1_i1	wt_GSNO	wt_ph8	-0.702510801497461	14.6355179638282	5.62335492840333e-11	3.133012031539e-10
+TR2278|c0_g1_i1	wt_GSNO	wt_ph8	0.490901034745758	15.2921454021456	1.53296499052609e-09	7.47320432881468e-09
+TR24|c0_g1_i1	wt_GSNO	wt_ph8	-2.16007337608378	13.5636496776551	8.67157466173412e-09	3.75768235341812e-08
+TR5075|c0_g1_i1	wt_GSNO	wt_ph8	-3.7524485458028	12.8683202800317	5.50095216588421e-08	2.14537134469484e-07
+TR4669|c0_g2_i1	wt_GSNO	wt_ph8	10.4044948993067	13.1110475123695	1.35189372056785e-06	4.79307773655872e-06
+TR3788|c0_g1_i1	wt_GSNO	wt_ph8	2.47698512550917	13.0240883091698	1.80487840553907e-05	5.86585481800198e-05
+TR1479|c0_g1_i1	wt_GSNO	wt_ph8	0.272661827455658	15.1172528121102	0.000483095512098729	0.00144928653629619
+TR1678|c0_g1_i1	wt_GSNO	wt_ph8	-3.02812287247775	9.36059212330112	0.0074853976481696	0.0208521791627582
+TR2107|c1_g1_i1	wt_GSNO	wt_ph8	1.98032359155541	9.36544178725855	0.0305238827180189	0.0756824353198294
+TR2844|c0_g1_i1	wt_GSNO	wt_ph8	0.244755727600329	14.4560017424587	0.0310492042337762	0.0756824353198294
+TR1859|c3_g1_i1	wt_GSNO	wt_ph8	-4.12978123132011	8.37588761488442	0.0428877609330621	0.0983895691993777
+TR3091|c0_g1_i1	wt_GSNO	wt_ph8	0.148576217250104	14.9963238698071	0.0547318692708507	0.11858571675351
+TR2672|c0_g1_i1	wt_GSNO	wt_ph8	-1.64029381826409	9.53984158811941	0.100507062957769	0.206303971334369
+TR4163|c0_g1_i1	wt_GSNO	wt_ph8	0.156926020788278	14.5006265631178	0.113620071038851	0.22155913852576
+TR4859|c0_g1_i1	wt_GSNO	wt_ph8	1.3062724221166	8.73091245897321	0.181160758857669	0.3364414093071
+TR4084|c0_g1_i1	wt_GSNO	wt_ph8	-0.390578563212142	13.8603174460746	0.270419882900116	0.479380701504752
+TR1982|c2_g1_i1	wt_GSNO	wt_ph8	-0.866592651710305	10.0958159836705	0.312186869456376	0.515984430920105
+TR1894|c2_g1_i1	wt_GSNO	wt_ph8	0.989932992780787	8.78384403630691	0.317528880566218	0.515984430920105
+TR4277|c0_g1_i1	wt_GSNO	wt_ph8	0.107189584823599	14.0046148411409	0.347278576725125	0.541754579691195
+TR2487|c0_g1_i1	wt_GSNO	wt_ph8	0.0467513454249246	16.526653433485	0.376403968202147	0.560230359736405
+TR3249|c0_g1_i1	wt_GSNO	wt_ph8	-1.00369455926223	9.08504250192555	0.387851787509819	0.560230359736405
+TR5212|c0_g1_i1	wt_GSNO	wt_ph8	0.310409394484433	13.3365591825697	0.416163942507532	0.572783249883747
+TR2011|c5_g1_i1	wt_GSNO	wt_ph8	0.799376994792807	9.70509536731836	0.425915749913555	0.572783249883747
+TR1837|c2_g1_i1	wt_GSNO	wt_ph8	0.59484087321072	8.66193471010726	0.588495494688377	0.76504414309489
+TR2090|c0_g1_i1	wt_GSNO	wt_ph8	0.766971023107968	9.89421471118339	0.638322407555079	0.8030507707951
+TR131|c0_g1_i1	wt_GSNO	wt_ph8	0.0187996511046741	17.0827735361623	0.697507705031756	0.850087515507453
+TR1122|c0_g1_i1	wt_GSNO	wt_ph8	0.908051089281089	8.22928258978683	0.753364106379395	0.890339398448377
+TR1449|c0_g1_i1	wt_GSNO	wt_ph8	-0.0452741219590205	13.4583026590017	0.919111339143084	1
+TR939|c0_g1_i1	wt_GSNO	wt_ph8	0.0309689709592036	13.3146949564453	0.956245904999637	1
+TR5055|c0_g2_i1	wt_GSNO	wt_ph8	-0.0548476287872344	9.62768102188797	0.999999999999985	1
+TR2182|c3_g2_i6	wt_GSNO	wt_ph8	-0.517423422896207	8.5297276065799	1	1
+TR127|c1_g1_i1	wt_GSNO	wt_ph8	-0.299043611515333	8.4576897025083	1	1
+TR3807|c0_g1_i1	wt_GSNO	wt_ph8	0.266132577378544	7.94319410024963	1	1
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results	Thu Jun 14 03:12:12 2018 -0400
@@ -1,40 +1,40 @@
-logFC	logCPM	PValue	FDR
-TR2779|c0_g1_i1	2.23795519272237	15.9076254017254	2.92187316761645e-09	1.13953053537042e-07
-TR1492|c0_g1_i2	-0.807554446371668	16.8426446227048	5.58321346448906e-08	1.08872662557537e-06
-TR24|c0_g1_i1	2.16839334936064	13.5222768601527	3.73856822091501e-07	4.86013868718952e-06
-TR3788|c0_g1_i1	-2.47096654484901	13.0144557887788	1.245732049043e-06	9.71670998253539e-06
-TR5075|c0_g1_i1	3.68481140303272	12.7944067233298	3.44359702134355e-06	2.23833806387331e-05
-TR3854|c0_g1_i1	-0.290746293924475	17.7782076349597	5.25322144866517e-07	5.12189091244854e-06
-TR1891|c0_g1_i1	1.35768165107067	14.6117632515968	5.28666359293828e-06	2.79053243123467e-05
-TR4761|c0_g1_i1	0.878920056028248	14.8002262876656	5.72416908971214e-06	2.79053243123467e-05
-TR2122|c0_g2_i2	0.730166040402744	14.7551588447381	0.000213340170514583	0.000924474072229861
-TR3638|c0_g1_i1	0.708321413581678	14.6195575978943	0.000258928735946659	0.00100982207019197
-TR2107|c1_g1_i1	-1.90861736829884	8.90712643491077	0.00457979737107378	0.0148843414559898
-TR1678|c0_g1_i1	2.86408187112217	8.67828416118206	0.00614682516189	0.01844047548567
-TR2278|c0_g1_i1	-0.503051556783977	15.2850549214884	0.00155857674629228	0.00552586300958173
-TR1859|c3_g1_i1	1.96144637998691	6.77065030795652	0.0428269385052548	0.0982500353944082
-TR2672|c0_g1_i1	1.69730734417424	8.97832173338033	0.0866262290356731	0.160877282494822
-TR1479|c0_g1_i1	-0.277933522953326	15.1098597149167	0.0157877120065803	0.0439800548754737
-TR1982|c2_g1_i1	0.859948395691952	9.74982883974683	0.0845253825418736	0.160877282494822
-TR4859|c0_g1_i1	-1.04376243585308	7.84838377560073	0.178339170085147	0.289801151388364
-TR2011|c5_g1_i1	-0.835627288758852	9.33803398810951	0.117576176969539	0.20843049553691
-TR4084|c0_g1_i1	0.383433512314591	13.8345091917852	0.0320674039619619	0.083375250301101
-TR1894|c2_g1_i1	-0.899367664455804	7.86698528437277	0.236693956821629	0.369242572641742
-TR5212|c0_g1_i1	-0.317453614519532	13.3093804544918	0.0408068910563242	0.0982500353944082
-TR2182|c3_g2_i6	0.988859576038597	7.34392475064937	0.332144974966109	0.462630500845651
-TR3249|c0_g1_i1	1.18548803762213	8.36747688877935	0.296376188714782	0.444564283072173
-TR1837|c2_g1_i1	-0.83411458992077	7.6102620160458	0.393260306376011	0.528867308574635
-TR3807|c0_g1_i1	-0.40219136988549	5.09566487188118	0.681998347783062	0.765740423023185
-TR4669|c0_g2_i1	-6.05037553674292	13.1239272719772	0.480074268471172	0.603964402270185
-TR1122|c0_g1_i1	-0.184244267394782	6.64199260311611	0.869699168726351	0.892585988955992
-TR127|c1_g1_i1	0.354388761220407	7.15556768591471	0.687202943738756	0.765740423023185
-TR2844|c0_g1_i1	-0.251980888130202	14.4425124782726	0.0594765231313145	0.128865800117848
-TR2090|c0_g1_i1	0.862128177746631	9.64998833298881	0.646749723219784	0.764340581987017
-TR3091|c0_g1_i1	-0.148831558112849	14.9878570236746	0.0841354210369957	0.160877282494822
-TR5055|c0_g2_i1	-0.0583511298028353	9.18288041060754	0.918331019801174	0.918331019801174
-TR4163|c0_g1_i1	-0.161834057105857	14.4879250602579	0.126768900432688	0.214955961603254
-TR4277|c0_g1_i1	-0.103273026252208	13.9874746529507	0.30829078508145	0.445308911784317
-TR939|c0_g1_i1	-0.0333503331526365	13.2856573711711	0.715260879184748	0.774865952450143
-TR1449|c0_g1_i1	0.049884213852527	13.4293306544833	0.75234222467997	0.793009371959969
-TR2487|c0_g1_i1	-0.0480185034754555	16.5239765307922	0.407818984620182	0.530164680006236
-TR131|c0_g1_i1	-0.0203187870937255	17.0810493411762	0.539920494505425	0.658028102678487
+sampleA	sampleB	logFC	logCPM	PValue	FDR
+TR2779|c0_g1_i1	wt_GSNO	wt_ph8	-2.23795519272237	15.9076254017254	2.92187316761645e-09	1.13953053537042e-07
+TR1492|c0_g1_i2	wt_GSNO	wt_ph8	0.807554446371668	16.8426446227048	5.58321346448906e-08	1.08872662557537e-06
+TR24|c0_g1_i1	wt_GSNO	wt_ph8	-2.16839334936064	13.5222768601527	3.73856822091501e-07	4.86013868718952e-06
+TR3788|c0_g1_i1	wt_GSNO	wt_ph8	2.47096654484901	13.0144557887788	1.245732049043e-06	9.71670998253539e-06
+TR5075|c0_g1_i1	wt_GSNO	wt_ph8	-3.68481140303272	12.7944067233298	3.44359702134355e-06	2.23833806387331e-05
+TR3854|c0_g1_i1	wt_GSNO	wt_ph8	0.290746293924475	17.7782076349597	5.25322144866517e-07	5.12189091244854e-06
+TR1891|c0_g1_i1	wt_GSNO	wt_ph8	-1.35768165107067	14.6117632515968	5.28666359293828e-06	2.79053243123467e-05
+TR4761|c0_g1_i1	wt_GSNO	wt_ph8	-0.878920056028248	14.8002262876656	5.72416908971214e-06	2.79053243123467e-05
+TR2122|c0_g2_i2	wt_GSNO	wt_ph8	-0.730166040402744	14.7551588447381	0.000213340170514583	0.000924474072229861
+TR3638|c0_g1_i1	wt_GSNO	wt_ph8	-0.708321413581678	14.6195575978943	0.000258928735946659	0.00100982207019197
+TR2107|c1_g1_i1	wt_GSNO	wt_ph8	1.90861736829884	8.90712643491077	0.00457979737107378	0.0148843414559898
+TR1678|c0_g1_i1	wt_GSNO	wt_ph8	-2.86408187112217	8.67828416118206	0.00614682516189	0.01844047548567
+TR2278|c0_g1_i1	wt_GSNO	wt_ph8	0.503051556783977	15.2850549214884	0.00155857674629228	0.00552586300958173
+TR1859|c3_g1_i1	wt_GSNO	wt_ph8	-1.96144637998691	6.77065030795652	0.0428269385052548	0.0982500353944082
+TR2672|c0_g1_i1	wt_GSNO	wt_ph8	-1.69730734417424	8.97832173338033	0.0866262290356731	0.160877282494822
+TR1479|c0_g1_i1	wt_GSNO	wt_ph8	0.277933522953326	15.1098597149167	0.0157877120065803	0.0439800548754737
+TR1982|c2_g1_i1	wt_GSNO	wt_ph8	-0.859948395691952	9.74982883974683	0.0845253825418736	0.160877282494822
+TR4859|c0_g1_i1	wt_GSNO	wt_ph8	1.04376243585308	7.84838377560073	0.178339170085147	0.289801151388364
+TR2011|c5_g1_i1	wt_GSNO	wt_ph8	0.835627288758852	9.33803398810951	0.117576176969539	0.20843049553691
+TR4084|c0_g1_i1	wt_GSNO	wt_ph8	-0.383433512314591	13.8345091917852	0.0320674039619619	0.083375250301101
+TR1894|c2_g1_i1	wt_GSNO	wt_ph8	0.899367664455804	7.86698528437277	0.236693956821629	0.369242572641742
+TR5212|c0_g1_i1	wt_GSNO	wt_ph8	0.317453614519532	13.3093804544918	0.0408068910563242	0.0982500353944082
+TR2182|c3_g2_i6	wt_GSNO	wt_ph8	-0.988859576038597	7.34392475064937	0.332144974966109	0.462630500845651
+TR3249|c0_g1_i1	wt_GSNO	wt_ph8	-1.18548803762213	8.36747688877935	0.296376188714782	0.444564283072173
+TR1837|c2_g1_i1	wt_GSNO	wt_ph8	0.83411458992077	7.6102620160458	0.393260306376011	0.528867308574635
+TR3807|c0_g1_i1	wt_GSNO	wt_ph8	0.40219136988549	5.09566487188118	0.681998347783062	0.765740423023185
+TR4669|c0_g2_i1	wt_GSNO	wt_ph8	6.05037553674292	13.1239272719772	0.480074268471172	0.603964402270185
+TR1122|c0_g1_i1	wt_GSNO	wt_ph8	0.184244267394782	6.64199260311611	0.869699168726351	0.892585988955992
+TR127|c1_g1_i1	wt_GSNO	wt_ph8	-0.354388761220407	7.15556768591471	0.687202943738756	0.765740423023185
+TR2844|c0_g1_i1	wt_GSNO	wt_ph8	0.251980888130202	14.4425124782726	0.0594765231313145	0.128865800117848
+TR2090|c0_g1_i1	wt_GSNO	wt_ph8	-0.862128177746631	9.64998833298881	0.646749723219784	0.764340581987017
+TR3091|c0_g1_i1	wt_GSNO	wt_ph8	0.148831558112849	14.9878570236746	0.0841354210369957	0.160877282494822
+TR5055|c0_g2_i1	wt_GSNO	wt_ph8	0.0583511298028353	9.18288041060754	0.918331019801174	0.918331019801174
+TR4163|c0_g1_i1	wt_GSNO	wt_ph8	0.161834057105857	14.4879250602579	0.126768900432688	0.214955961603254
+TR4277|c0_g1_i1	wt_GSNO	wt_ph8	0.103273026252208	13.9874746529507	0.30829078508145	0.445308911784317
+TR939|c0_g1_i1	wt_GSNO	wt_ph8	0.0333503331526365	13.2856573711711	0.715260879184748	0.774865952450143
+TR1449|c0_g1_i1	wt_GSNO	wt_ph8	-0.049884213852527	13.4293306544833	0.75234222467997	0.793009371959969
+TR2487|c0_g1_i1	wt_GSNO	wt_ph8	0.0480185034754555	16.5239765307922	0.407818984620182	0.530164680006236
+TR131|c0_g1_i1	wt_GSNO	wt_ph8	0.0203187870937255	17.0810493411762	0.539920494505425	0.658028102678487
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
Binary file test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf has changed
Binary file test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf has changed
Binary file test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf has changed
Binary file test-data/count/qcheck/wt_37.rep_compare.pdf has changed
Binary file test-data/count/qcheck/wt_ph8.rep_compare.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity_paired_unmerged_1.fasta	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,14 @@
+>TRINITY_DN2_c0_g1_i1 len=229 path=[0:0-228]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN1_c0_g1_i1 len=380 path=[0:0-379]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
+>TRINITY_DN3_c0_g1_i1 len=669 path=[0:0-668]
+GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN3_c0_g2_i1 len=279 path=[0:0-278]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN3_c0_g3_i1 len=240 path=[0:0-239]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN3_c0_g4_i1 len=202 path=[0:0-201]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
+>TRINITY_DN0_c0_g1_i1 len=216 path=[0:0-215]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity_paired_unmerged_1.map	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,7 @@
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1
+TRINITY_DN3_c0_g2	TRINITY_DN3_c0_g2_i1
+TRINITY_DN3_c0_g3	TRINITY_DN3_c0_g3_i1
+TRINITY_DN3_c0_g4	TRINITY_DN3_c0_g4_i1
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1
--- a/test-data/raw/Trinity.fasta	Mon Jan 22 11:28:19 2018 -0500
+++ b/test-data/raw/Trinity.fasta	Thu Jun 14 03:12:12 2018 -0400
@@ -43,4 +43,3 @@
 CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
 ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
 TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity_single_unmerged_1.fasta	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,2 @@
+>TRINITY_DN0_c0_g1_i1 len=226 path=[0:0-225]
+CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity_single_unmerged_1.map	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,1 @@
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/supertranscripts/trinity_genes.fasta	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,14 @@
+>TRINITY_DN1_c0_g1
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN2_c2_g1
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/supertranscripts/trinity_genes.gtf	Thu Jun 14 03:12:12 2018 -0400
@@ -0,0 +1,14 @@
+TRINITY_DN1_c0_g1	Trinity_gene	exon	1	380	.	+	.	gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1"
+
+TRINITY_DN0_c0_g1	Trinity_gene	exon	1	229	.	+	.	gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1"
+
+TRINITY_DN2_c0_g1	Trinity_gene	exon	1	279	.	+	.	gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1"
+
+TRINITY_DN2_c1_g1	Trinity_gene	exon	1	541	.	+	.	gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1"
+
+TRINITY_DN2_c2_g1	Trinity_gene	exon	1	240	.	+	.	gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1"
+
+TRINITY_DN2_c3_g1	Trinity_gene	exon	1	202	.	+	.	gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1"
+
+TRINITY_DN3_c0_g1	Trinity_gene	exon	1	216	.	+	.	gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1"
+