# HG changeset patch
# User pmac
# Date 1464767991 14400
# Node ID 7ecbc3ec2f550d58b475bdb19361d22b300d8b7a

Uploaded

diff -r 000000000000 -r 7ecbc3ec2f55 robustZScoreNormalization.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/robustZScoreNormalization.pl	Wed Jun 01 03:59:51 2016 -0400
@@ -0,0 +1,76 @@
+###############################################################################
+# In summary this script calculates the robust z score for one or more plates
+# of data.
+#
+# Args:
+#   input.data.frame contains one or more columns of plate data. The first column 
+#   must contain the well annotation ie A01, A02 etc. Each subsequent column represents
+#   a plate of data where the column name is the plate name.
+#
+#   plate.conf.data.frame is a file of the following format:
+#	  well, type (syntax must be either "poscontr" or "negcontr" or "empty"), name (name of control)
+#
+# Returns:
+#    robust z score normalized values per plate.
+#
+# Author: kate gould
+###############################################################################
+
+use strict;
+use warnings;
+use IO::Handle;
+use File::Temp qw/ tempfile tempdir /;
+my $tdir = tempdir( CLEANUP => 0 );
+
+# check to make sure having correct input and output files
+my $usage = "usage: robustZScoreNormalization.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n";
+die $usage unless @ARGV == 3;
+
+#get the input arguments
+my $plateData = $ARGV[0];
+my $plateConfig =  $ARGV[1];
+my $zNorm =  $ARGV[2];
+
+#open the input files
+open (INPUT1, "<", $plateData) || die("Could not open file $plateData \n");
+open (INPUT2, "<", $plateConfig) || die("Could not open file $plateConfig \n");
+open (OUTPUT1, ">", $zNorm) || die("Could not open file $zNorm \n");
+
+#variable to store the name of the R script file
+my $r_script;
+
+# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values 	
+# construct an R script file and save it in a temp directory
+chdir $tdir;
+$r_script = "robustZScoreNormalization.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; 
+print Rcmd "
+	#options(show.error.messages = FALSE);
+	header <- read.table(\"$plateData\", head=F, sep=\"\\t\", comment=\"\", nrows=1);
+	input.data.frame <- read.table(\"$plateData\", head=F, sep=\"\\t\", skip=1);
+	plate.conf.data.frame <- read.table(\"$plateConfig\", head=T, sep=\"\\t\", comment=\"\");
+
+	# assumed second column is type ie negcontr or poscontr and third column is name of control
+	excluded.wells <- unique(plate.conf.data.frame[,1])
+	
+	robust.z.score.normalise <- function(x, y) return ((x-median(y))/mad(y))
+	robust.z.score.normalisation.data.frame <- data.frame(well=input.data.frame[,1], stringsAsFactors=FALSE)
+	
+	for (i in 2:length(colnames(input.data.frame))){
+		replicate.sample.values <- input.data.frame[((!(input.data.frame[,1] %in% excluded.wells))&(!(is.na(input.data.frame[,i])))),][,i]
+		robust.z.score.normalisation.data.frame <- cbind(robust.z.score.normalisation.data.frame, round(sapply(input.data.frame[,i], FUN=robust.z.score.normalise, replicate.sample.values), 2))
+	}
+	names(robust.z.score.normalisation.data.frame) <- names(input.data.frame)
+	write.table(header, file=\"$zNorm\", quote=F, sep=\"\\t\", row.names=F, col.names=F);
+	write.table(robust.z.score.normalisation.data.frame, file=\"$zNorm\", quote=F, sep=\"\\t\", row.names=F, col.names=F, append=T);
+	#eof\n";
+
+close Rcmd;	
+
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+
+#close the input and output files
+close(OUTPUT1);
+close(INPUT1);
+close(INPUT2);
diff -r 000000000000 -r 7ecbc3ec2f55 robustZScoreNormalization.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/robustZScoreNormalization.xml	Wed Jun 01 03:59:51 2016 -0400
@@ -0,0 +1,137 @@
+<tool id="robustZScoreNormalization" name="Calculate Robust Z Score Normalization" version="1.0.0">
+  <description>Per Plate</description>
+  
+  <command interpreter="perl">
+  	robustZScoreNormalization.pl $inputFile1 $inputFile2 $outputFile1
+  </command>
+
+  <inputs>
+  	<param format="tabular" name="inputFile1" type="data" label="Select the linear plates file"/>
+  	<param format="tabular" name="inputFile2" type="data" label="Select the plate configuration file"/>
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="outputFile1"/>
+  </outputs>
+
+  <tests>
+     <test>
+       <param name="inputFile1" value="150615-HR-12015-01A.linear"/>
+       <param name="inputFile2" value="plate_config.txt"/>
+       <output name="outputFile1" file="calc_robust_z.tabular"/> 
+     </test>
+  </tests>
+
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+This program takes a linear plate table and a plate config file as input and then performs Robust Z Score Normalization on the data.
+The plate config file **must** contain the columns Well, Type and Name in that order. Further the data in column Type must be **exclude**, **negcontr** or **poscontr**.
+
+**Example**
+
+If the plates table consisted of::
+
+	#Well	Table_1	Table_2
	A01	1654	6
	A02	1719	8
	A03	1624	19
	A04	1518	6
	A05	1587	12
	A06	1517	8
	A07	1638	9
	A08	1733	7
	A09	1617	6
	A10	1722	8
	...
+	P14	1630	6
	P15	1576	6
	P16	1740	7
	P17	1578	6
	P18	1544	6
	P19	1692	6
	P20	1560	6
	P21	1552	6
	P22	1790	7
	P23	1537	6
	P24	NA	NA
+	
+and the plates config was::
+	
+	#Well	Type	Name
	A02	negcontr	NT2
+	B02	negcontr	NT2
+	C02	poscontr	ASCIZ
+	D02	poscontr	PARP
+	E02	negcontr	NT2
+	F02	poscontr	ASCIZ
+	G02	poscontr	PARP
+	H02	negcontr	NT2
+	I02	poscontr	ASCIZ
+	J02	poscontr	PARP
+	K02	negcontr	NT2
+	L02	poscontr	ASCIZ
+	M02	poscontr	PARP
+	N02	negcontr	NT2
+	O02	poscontr	ASCIZ
+	P02	negcontr	NT2
+	A23	negcontr	NT2
+	B23	negcontr	NT2
+	C23	poscontr	ASCIZ
+	D23	poscontr	PARP
+	E23	negcontr	NT2
+	F23	poscontr	ASCIZ
+	G23	poscontr	PARP
+	H23	negcontr	NT2
+	I23	poscontr	ASCIZ
+	J23	poscontr	PARP
+	K23	negcontr	NT2
+	L23	poscontr	ASCIZ
+	M23	poscontr	PARP
+	N23	negcontr	NT2
+	O23	poscontr	ASCIZ
+	P23	negcontr	NT2
+	A01	exclude	exclude
+	A24	exclude	exclude
+	B01	exclude	exclude
+	B24	exclude	exclude
+	C01	exclude	exclude
+	C24	exclude	exclude
+	D01	exclude	exclude
+	D24	exclude	exclude
+	E01	exclude	exclude
+	E24	exclude	exclude
+	F01	exclude	exclude
+	F24	exclude	exclude
+	G01	exclude	exclude
+	G24	exclude	exclude
+	H01	exclude	exclude
+	H24	exclude	exclude
+	I01	exclude	exclude
+	I24	exclude	exclude
+	J01	exclude	exclude
+	J24	exclude	exclude
+	K01	exclude	exclude
+	K24	exclude	exclude
+	L01	exclude	exclude
+	L24	exclude	exclude
+	M01	exclude	exclude
+	M24	exclude	exclude
+	N01	exclude	exclude
+	N24	exclude	exclude
+	O01	exclude	exclude
+	O24	exclude	exclude
+	P01	exclude	exclude
+	P24	exclude	exclude
+	
+Running the program will give the following output::
+
+	#Well	Table_1	Table_2
+	A01	0.74	-0.67
+	A02	1.55	0.67
+	A03	0.36	8.09
+	A04	-0.96	-0.67
+	A05	-0.1	3.37
+	A06	-0.97	0.67
+	A07	0.54	1.35
+	A08	1.72	0
+	A09	0.27	-0.67
+	A10	1.59	0.67
+	...
+	P14	0.44	-0.67
+	P15	-0.24	-0.67
+	P16	1.81	0
+	P17	-0.21	-0.67
+	P18	-0.64	-0.67
+	P19	1.21	-0.67
+	P20	-0.44	-0.67
+	P21	-0.54	-0.67
+	P22	2.44	0
+	P23	-0.72	-0.67
+	P24	NA	NA
+
+  </help>  
+  
+</tool>
diff -r 000000000000 -r 7ecbc3ec2f55 test-data/150615-HR-12015-01A.linear
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/150615-HR-12015-01A.linear	Wed Jun 01 03:59:51 2016 -0400
@@ -0,0 +1,385 @@
+#Well	Table_1	Table_2	Table_3	Table_4	Table_5	Table_6
+A01	2215	8.88	55.62	2.57	2.91	78.76
+A02	2811	8.61	57.35	1.07	2.03	63.32
+A03	2226	10.96	70.4	0.54	2.41	79.41
+A04	2528	9.35	61.59	1.66	2.14	74.9
+A05	1827	11.87	73.78	0.66	2.27	79.31
+A06	2337	8.69	58.49	1.07	1.87	62.34
+A07	2233	9.7	63.41	1.07	2.32	77.48
+A08	2462	8.48	57.39	1.06	2.07	67.32
+A09	2790	9.5	62.83	1.65	2.52	80.57
+A10	2792	9.19	60.67	1.9	2.38	73.6
+A11	2547	9.51	61.76	1.33	2.8	84.6
+A12	2629	9.47	60.94	2.09	2.42	72.34
+A13	1655	11.8	71.24	0.85	2.3	71.88
+A14	2647	8.27	52.13	2.15	2.37	72.76
+A15	2300	11.5	72.17	0.57	2.68	86.26
+A16	2030	11.71	71.63	0.74	2.66	89.03
+A17	2124	9.78	63.89	1.13	2.45	81.13
+A18	2461	9.14	59.65	1.83	2.3	77.14
+A19	2273	8.68	57.85	0.97	2.32	69.57
+A20	2281	10.62	70.58	0.7	1.98	65.3
+A21	2412	10.49	69.86	0.46	2.07	70.27
+A22	1331	10.72	69.65	0.68	1.97	61.54
+A23	2245	9.88	66.24	0.4	2.17	66.33
+A24	2037	8.13	53.26	1.42	2.06	70.05
+B01	2184	10.31	65.29	0.87	2.33	72.4
+B02	2104	9.33	57.94	3.09	2.44	79.26
+B03	1639	11.13	69.68	0.55	2.03	67.42
+B04	2467	9.84	64.33	0.77	2.03	67.95
+B05	1818	11.75	75.25	0.66	1.97	68.96
+B06	1769	9.08	57.32	2.43	2.29	69.18
+B07	1654	12.22	75.7	0.6	2.14	75.29
+B08	2199	10.04	68.58	0.73	2.43	73.55
+B09	2043	8.74	59.03	1.22	1.96	57.65
+B10	1329	11.6	73.06	0.68	2.04	58.75
+B11	2533	7.31	47.06	3.83	3.01	95.3
+B12	2712	9.31	61.98	2.06	2.49	75.2
+B13	1824	10.83	68.42	1.54	2.45	80.09
+B14	2718	7.68	49.74	4.01	2.54	81.37
+B15	2443	10.4	68.81	1.02	2.64	91.33
+B16	2061	11.82	77.1	0.39	2.53	87.74
+B17	2088	10.83	70.69	0.62	2.22	74.12
+B18	2730	10.36	70.4	0.81	2.39	78.69
+B19	2279	8.09	54.28	1.14	1.98	61.28
+B20	2371	12.37	78.28	0.25	2.23	78.36
+B21	2114	10.49	71.85	0.85	2.32	73.66
+B22	2355	9.84	66.71	0.72	2.04	64.63
+B23	1154	11.75	72.1	0.35	2.35	65.16
+B24	1646	7.49	50.12	1.82	2.11	64.74
+C01	2356	9.67	64.43	1.02	2.07	61.55
+C02	2680	10.27	67.57	0.82	2.03	60.64
+C03	2305	8.51	55.88	1.56	1.87	56.38
+C04	2510	9.55	63.55	1	2.02	58.22
+C05	2650	10.23	67.96	0.3	1.95	59.48
+C06	2918	9.76	64.98	0.69	2.21	65.35
+C07	2618	8.28	55.39	1.26	2.42	68.98
+C08	2654	9.56	65.3	1.09	2.52	75.17
+C09	2828	8.44	57.39	1.34	2.21	63.59
+C10	2877	9.48	64.75	1.32	2.59	77.38
+C11	2441	9.78	65.38	1.47	2.38	73.63
+C12	2870	7.1	47.04	3.69	2.87	88.54
+C13	3202	9.02	59.93	1.72	2.43	78.2
+C14	2619	8.63	57.43	2.1	2.93	95.11
+C15	2716	8.82	58.73	1.18	2.46	78.45
+C16	2413	10.72	71.07	0.33	2.62	84.52
+C17	2893	8.18	56.14	1.52	2.8	83.32
+C18	2669	9.82	66.62	0.67	2.26	70.88
+C19	2272	10.81	71.79	0.79	2.1	68.8
+C20	2161	9.42	63.4	1.2	2.79	79.7
+C21	2677	8.75	59.62	0.78	2.04	62.52
+C22	2406	9.91	65	0.71	2.08	68.61
+C23	2494	7.54	49.44	2.33	2.25	63.14
+C24	1760	7.85	51.99	1.82	2.15	66.92
+D01	2206	7.2	45.01	2.77	1.41	36.44
+D02	1033	10.08	62.25	1.84	2.61	77.42
+D03	1744	7.58	49.14	3.04	2.4	70.59
+D04	2579	8.78	59.83	1.2	2.12	62.68
+D05	1921	9.41	64.08	0.94	2.29	70.86
+D06	2352	9.68	63.95	2.3	2.6	79.33
+D07	1844	8.86	59.06	2.11	2.76	85.21
+D08	2831	8.45	56.55	1.77	2.62	78
+D09	1803	9.59	63.67	1.22	2.81	84.73
+D10	2531	9.03	59.9	1.78	2.64	75.75
+D11	1942	7.37	48.51	3.24	3.1	95.33
+D12	2653	9.72	66.34	1.43	2.77	84.49
+D13	2624	6.77	43.52	4.54	3.06	101.35
+D14	2777	6.68	43.03	5.47	3.36	106.95
+D15	2523	8.53	58.7	1.43	3.13	101.22
+D16	2532	9.9	66.11	0.87	2.96	89.01
+D17	2243	9.92	66.79	0.76	3.15	105.74
+D18	2653	11.31	76.1	0.45	2.67	85.7
+D19	1806	11.24	73.26	0.44	2.77	90.06
+D20	2502	11.17	74.5	0.48	2.58	76.4
+D21	2355	9.81	67.22	0.85	2.69	88.68
+D22	2036	11.95	77.65	0.29	2.54	82.78
+D23	4	19.75	100	0	1.5	74.25
+D24	2056	7.06	45.82	1.9	2.27	76.56
+E01	1953	7.89	52.02	2.36	2.09	64.14
+E02	58	10.38	67.24	6.9	2.34	81.33
+E03	1429	11	70.89	0.91	2.09	65.5
+E04	2419	9.41	61.06	1.2	2.4	69.87
+E05	2326	9.41	62.64	1.25	2.36	69.72
+E06	2281	9.32	61.03	2.59	2.88	89.16
+E07	2524	7.92	52.61	2.73	2.63	78
+E08	2444	9.17	62.19	1.51	2.8	84.21
+E09	2402	9.13	60.95	1.5	2.6	78.8
+E10	2470	9.23	60.89	1.94	2.64	78.64
+E11	2387	9.57	63.3	1.59	2.58	80.7
+E12	2812	9.54	64.76	1.21	2.61	83.54
+E13	2121	9.11	60.68	2.22	2.37	70.04
+E14	2467	8.67	58.25	1.34	2.65	87.2
+E15	1932	6.3	39.23	5.64	2.89	91.38
+E16	2207	9.54	63.57	1.54	2.63	86.13
+E17	866	11.03	69.98	0.81	2.23	71.41
+E18	1665	8.31	55.56	2.34	3.14	93.34
+E19	1668	11.19	72.96	0.66	2.3	73.16
+E20	1942	10.59	70.19	0.46	2.46	76.69
+E21	2717	10.46	69.82	0.44	2.22	72.24
+E22	1995	9.92	67.27	1.45	2.73	86.76
+E23	2686	8.98	60.65	1.19	2.33	71.8
+E24	1711	8.25	53.71	1.81	2.43	78.22
+F01	2647	8.61	56.89	1.44	2.05	56.86
+F02	1866	10.14	66.4	0.91	1.86	55.02
+F03	2327	7.3	46.41	4.08	2.04	60.29
+F04	1831	6.3	39.16	6.66	2.25	67.66
+F05	2081	8.89	57.33	2.4	2.34	70.01
+F06	2360	9.29	62.12	2.54	2.41	77.11
+F07	2465	8.21	54.36	2.92	2.59	77.73
+F08	2561	7.36	49	2.89	2.31	66.52
+F09	2242	9.81	66.77	1.43	2.47	72.7
+F10	2595	6.08	37.5	6.2	2.39	68.73
+F11	2601	8.19	54.48	3.65	2.77	96.56
+F12	2075	9.72	63.04	1.59	2.47	72.8
+F13	2452	9.25	62.11	1.51	2.66	82.33
+F14	2506	8.22	53.79	2.04	2.54	77.56
+F15	2228	8.19	53.82	2.65	2.91	103.54
+F16	2869	7.83	52.49	1.92	2.58	76.14
+F17	1322	8.78	60.14	1.97	2.52	72.6
+F18	2712	7.56	50	3.39	2.68	81.09
+F19	2623	9	60.62	1.03	2.41	73.71
+F20	2320	9.37	62.5	1.51	2.43	70.9
+F21	2528	9.04	59.53	1.15	2.2	65.33
+F22	1797	6.44	39.96	4.67	2.38	70.58
+F23	1933	10.26	67.36	0.93	2.5	71.62
+F24	1759	8.4	56.17	1.99	1.92	67.93
+G01	2715	10.83	72.08	0.59	1.98	58.65
+G02	2567	11.22	71.76	0.51	1.95	59.34
+G03	2346	8.73	57.37	1.49	2.13	61.93
+G04	2536	7.29	46.77	4.89	2.24	65.72
+G05	2157	8.33	54.38	2.23	2.35	65.99
+G06	2549	6.64	41.66	5.1	2.59	78.36
+G07	2368	9.22	61.15	1.35	2.41	73.63
+G08	2798	9.61	63.44	1.18	2.46	72.8
+G09	2595	8.97	59.73	1.93	2.4	68.47
+G10	3309	6.57	42.16	3.84	2.34	62.92
+G11	2701	7.84	53.05	2.3	2.46	68.96
+G12	2916	7.37	49.04	3.19	2.61	72.96
+G13	2664	9.26	63.48	1.73	2.88	88.03
+G14	2998	7.58	51.17	2.94	2.6	75.25
+G15	2257	9.19	63.14	1.2	2.49	71.58
+G16	2850	10.29	70.53	1.09	2.33	71.99
+G17	2559	7.88	52.25	2.34	2.67	83.35
+G18	2684	8.49	55.48	2.72	2.69	83.61
+G19	2852	7.68	50.25	3.54	2.78	87.58
+G20	2779	7.11	45.88	3.17	2.58	73.2
+G21	2448	9.83	67.28	0.69	2.52	77.41
+G22	2741	7.4	48.23	3.1	2.42	68.04
+G23	2945	10.08	70.12	0.75	2.52	78.27
+G24	1740	6.25	38.91	3.33	2.19	65.21
+H01	2214	12.71	78.73	0.36	2.1	68.06
+H02	11	19.73	90.91	0	2.18	67.36
+H03	1344	10.4	65.77	1.86	2.36	69.92
+H04	1937	7.72	49.3	3.1	2.42	70.48
+H05	2130	9.08	60.19	1.41	2.39	67.18
+H06	2637	8.69	56.16	1.71	2.34	68.97
+H07	2278	10.21	67.08	1.14	2.85	85.95
+H08	2020	10.78	72.62	1.09	2.56	74.15
+H09	1780	10.32	67.25	1.91	3.05	82.88
+H10	2262	7.84	52.43	2.25	3.01	78.92
+H11	2130	12.63	80.47	0.47	3.17	96.52
+H12	2404	9.57	63.89	1.87	3.07	87.48
+H13	1872	10.9	70.78	1.23	3.15	91.34
+H14	2598	9.23	63.01	1.31	2.65	76.86
+H15	2164	10.57	72.87	1.06	2.74	78.64
+H16	2475	9.77	66.87	0.73	2.86	90.95
+H17	1783	11.15	72.74	0.67	2.97	88.69
+H18	2114	9.08	60.83	1.32	2.87	84.31
+H19	2621	7.59	49.83	3.13	2.69	81.29
+H20	2623	7.95	53.49	2.06	2.34	68.36
+H21	1954	10.2	66.27	1.64	2.5	78.56
+H22	2356	9.53	62.82	1.57	3.31	99.15
+H23	8	26	100	0	3.25	139
+H24	1421	7.88	47.64	4.93	1.98	78.52
+I01	2071	12.39	78.17	0.43	2.11	61.97
+I02	1366	12.04	75.62	0.88	2.36	65.33
+I03	1769	9.91	63.2	1.19	2.13	56.36
+I04	2389	10.75	70.24	0.63	2.28	65.29
+I05	1983	8	51.49	2.57	2.69	74.38
+I06	2209	9.97	64.46	1.45	2.9	80.24
+I07	2524	9.56	62.08	1.78	3.01	88.14
+I08	1961	11.84	75.68	0.66	3.23	88.78
+I09	1925	11.12	71.27	0.88	2.82	78.49
+I10	2364	10.85	69.42	0.89	3.17	89.68
+I11	1809	12.46	77.34	0.44	2.66	76.47
+I12	2387	10.95	70.38	0.88	3.15	87.18
+I13	2530	12.5	78.42	0.87	3.04	94.74
+I14	2086	12.23	75.6	0.91	3.47	101.93
+I15	2587	10.9	72.59	0.7	2.84	85.07
+I16	2480	12.24	78.15	0.44	3.45	108.16
+I17	1770	12.3	78.25	0.73	3.12	95.09
+I18	1964	8.3	55.09	2.9	3.32	96.99
+I19	1969	10.6	69.78	1.12	3.11	95.42
+I20	2330	8.19	53.22	2.1	3.43	100.06
+I21	1922	8.76	58.27	1.82	3.08	90.8
+I22	2062	11.61	75.12	0.58	3.06	95.76
+I23	2446	9.95	66.39	1.19	2.99	83.27
+I24	1457	9.09	57.79	2.2	3.49	102.71
+J01	1967	13.45	80.22	0.31	2.06	62
+J02	1954	11.02	71.65	1.23	2.08	57.26
+J03	1402	10.14	67.05	0.86	1.75	48.25
+J04	1316	10.69	70.82	0.68	2.08	59.11
+J05	1784	7	45.8	4.37	2.09	58.3
+J06	2557	7.78	52.33	2.66	2.73	77.66
+J07	1753	10.05	66.29	1.43	2.44	71.51
+J08	1844	11.57	75.43	0.98	2.59	73.92
+J09	1670	9.2	61.44	0.78	2.5	65.14
+J10	2427	9.55	64.19	1.03	2.68	75.03
+J11	2011	11.93	77.03	0.2	2.55	73.74
+J12	1973	11.51	74.71	0.91	2.92	82.11
+J13	2276	11.43	74.74	0.66	3	89.39
+J14	2088	11.24	74.47	0.67	2.94	87.12
+J15	2476	10.48	69.35	0.65	2.77	79.58
+J16	2395	10.95	71.9	0.92	3.22	94.31
+J17	2127	11.9	75.6	0.52	2.8	87.35
+J18	2341	9.92	66.21	0.94	3.11	93.03
+J19	1800	13.06	81.61	0.61	2.54	82.49
+J20	2368	8.52	56.88	1.56	2.67	79.25
+J21	2387	7.99	50.98	2.51	2.99	88.09
+J22	2309	10.5	70.12	0.52	2.64	80.93
+J23	822	8.44	55.6	2.68	3.41	88.31
+J24	1434	11.4	69.67	0.49	2.56	75.84
+K01	2652	8.11	53.96	1.58	1.72	47.85
+K02	209	14.67	84.69	0.96	1.77	51.87
+K03	2838	6.24	38.51	4.33	1.85	52.13
+K04	3001	9.71	65.98	1.03	1.95	56.69
+K05	2873	7.73	52.52	2.89	1.97	54.93
+K06	2327	7.32	47.53	3.52	2.19	61.63
+K07	2870	7.96	54.01	2.37	2.14	62.09
+K08	2914	7.98	53.98	2.16	2.34	64.88
+K09	3239	8.13	55.26	1.82	2.2	59.7
+K10	2663	9.31	62.04	1.05	2.27	60.76
+K11	3009	7.53	49.52	1.5	2.28	62.38
+K12	2521	9.74	65.01	1.19	2.64	71.55
+K13	2470	8.63	58.14	1.74	2.43	68.82
+K14	2648	11.19	73.3	0.6	2.69	79.57
+K15	2692	8.76	58.77	1.63	2.18	64.46
+K16	2915	10.94	72.45	0.51	2.83	83.73
+K17	2653	9.45	64.87	1.39	2.41	73.68
+K18	2661	8.63	57.31	2.37	3.24	86.86
+K19	2647	7.55	49.34	2.34	2.74	82.51
+K20	2221	10.27	69.29	1.44	3.22	93.3
+K21	1987	9.5	63.56	1.56	2.41	70.16
+K22	2557	9.32	60.62	2.11	3.64	108.95
+K23	2367	9.79	65.82	1.31	2.82	81.75
+K24	1498	9.08	58.88	1.94	2.74	86.15
+L01	2370	10.08	67.26	0.97	1.89	53.56
+L02	2240	10.54	68.53	1.12	1.89	56.19
+L03	1355	10.4	68.34	1.11	1.71	48.94
+L04	2608	10.09	67.75	1	2.14	61.59
+L05	2088	8.34	54.21	3.21	2.08	58.54
+L06	2332	9.22	61.62	1.97	2.29	66.29
+L07	1528	9.21	59.95	1.7	2.06	58.84
+L08	2352	9.47	63.95	1.66	2.14	60.65
+L09	2595	9.2	62.62	0.66	2.1	56.05
+L10	2135	8.54	55.64	1.73	2.23	57.12
+L11	2537	8.28	55.54	1.3	2.41	65.07
+L12	2348	11.87	76.11	0.38	2.63	78.84
+L13	2197	9.55	63.63	1.14	2.37	67.98
+L14	2411	10.23	68.56	0.91	2.61	76.71
+L15	2815	8.27	54.03	2.1	2.26	64.29
+L16	2498	8.88	58.93	1.44	2.24	64.05
+L17	2493	9.81	67.19	0.96	2.22	67.86
+L18	2709	8.11	53.78	2.03	2.2	60.62
+L19	2416	8.75	59.89	1.28	2.54	75.84
+L20	2081	10.65	69.1	0.62	2.25	72.08
+L21	2376	10.08	68.9	0.67	2.33	72.37
+L22	1528	7.56	48.3	3.99	2.6	77.79
+L23	2344	12.22	77.05	0.34	2.26	68.61
+L24	1646	9.04	58.81	1.7	1.8	55.4
+M01	2012	9.29	60.04	1.79	2.3	65.75
+M02	1813	11.41	72.31	0.77	2.2	66.88
+M03	1962	9.57	60.14	2.14	2.43	73.04
+M04	1816	11.38	72.91	0.88	2.07	66.33
+M05	2155	8.49	55.96	3.62	2.4	76.36
+M06	1993	11.24	75.01	0.85	1.94	63.19
+M07	2175	10.08	64.69	1.52	2.39	70.2
+M08	2309	10.12	67.43	1.17	2.16	65.42
+M09	2005	8.1	53.27	2.49	2.33	64.79
+M10	2786	9.29	62.1	1.4	2.45	66.01
+M11	2191	10.62	70.61	0.46	2.43	69.75
+M12	2571	10.68	70.48	0.51	2.23	66.84
+M13	2492	10.03	65.85	0.88	2.33	70.78
+M14	2326	10.11	66.38	0.86	2.51	73.36
+M15	2134	9.57	63.96	1.73	2.41	70.35
+M16	2637	9.38	63.56	1.63	2.36	68.77
+M17	2058	9.33	60.74	1.65	2.36	68.1
+M18	2428	9.96	65.98	0.66	2.42	72.35
+M19	1955	10.45	67.88	0.82	1.96	58.52
+M20	2349	8.09	53.34	2.68	2.76	83.89
+M21	2413	9.06	60.92	1.41	2.12	66.1
+M22	2398	10.66	71.18	0.75	2.4	73.38
+M23	2369	9.28	60.57	1.1	2.22	65.44
+M24	1753	7.99	52.48	2	2.31	73.49
+N01	2349	9.7	62.96	1.23	2	54.24
+N02	1100	9.78	65.64	1.91	2.11	59.64
+N03	1959	11.19	70.7	1.07	2.13	63.27
+N04	2547	9.07	60.35	1.53	2.17	60.21
+N05	1861	6.58	41.91	5.59	2.15	58.81
+N06	2667	7.91	50.69	3.11	2.25	62.86
+N07	2841	7.86	52.34	1.9	2.25	59.96
+N08	2090	9.2	60.53	2.11	2.45	68.68
+N09	2292	10.12	67.32	0.96	2.14	56.57
+N10	1988	8.68	57.8	1.51	2.37	60.56
+N11	1850	9.76	63.3	1.08	2.16	58.67
+N12	2692	9.25	62.33	0.74	2.27	62.41
+N13	2556	8.4	54.3	2.58	2.69	77.77
+N14	2718	6.73	42.9	3.42	2.63	70.67
+N15	1790	10.56	70.06	0.78	2.5	71.66
+N16	2357	10.09	68.65	0.89	2.38	71.39
+N17	1855	11.31	73.75	0.65	2.26	69.82
+N18	2912	9.07	61.81	1.17	2.43	70.12
+N19	2774	8.88	59.7	1.95	2.7	80.08
+N20	2244	7.66	51.16	3.03	2.61	72.69
+N21	2607	6.2	38.59	4.99	2.53	74.74
+N22	1606	10.13	66.63	1	2.57	75.63
+N23	2548	10.1	69.31	0.82	2.3	69.19
+N24	1885	8.58	57.93	1.86	2.42	76.91
+O01	2211	7.97	50.11	4.84	2.51	75.51
+O02	1992	10.62	66.16	2.11	1.97	57.64
+O03	2127	9.32	59.43	3.57	2.23	66.12
+O04	2209	11.3	71.57	0.91	2.08	62.99
+O05	2659	9.12	61.34	1.32	1.85	52.69
+O06	2635	8.44	54.99	3.19	2.32	68.44
+O07	2715	9.04	59.08	1.73	2.07	59.75
+O08	2380	8.6	58.24	1.39	2.08	54.5
+O09	2660	9.1	60.45	1.39	2.11	57.22
+O10	2754	9.46	63.62	1.6	2.16	59.51
+O11	2441	10.22	66.41	1.31	2.14	62.51
+O12	2149	10.7	68.96	1.07	1.98	56.79
+O13	1852	9.47	60.21	2	2.11	62.8
+O14	2402	10.61	68.53	0.67	2.25	70.24
+O15	2391	10.34	69.97	1.21	2.42	77.32
+O16	2544	9.71	62.62	1.42	2.23	65.64
+O17	2212	9.12	60.53	1.18	2.18	65.33
+O18	2282	8.64	57.27	2.76	2.5	70.41
+O19	2386	9.37	63.45	1.22	1.86	55.53
+O20	1851	8.95	59.75	1.24	1.93	53.9
+O21	2400	8.57	56.79	2.29	2.2	66.64
+O22	2414	9.52	63.92	1.33	2.3	66.6
+O23	2636	8.44	55.54	2.2	2.27	64.76
+O24	2115	6.49	40.28	4.4	2.68	77.69
+P01	1588	4.5	24.5	12.59	2.79	86.44
+P02	2169	5.6	32.6	6.22	2.01	52.67
+P03	1924	7.28	47.97	2.86	1.75	47.57
+P04	2189	7.91	50.57	2.7	1.82	51.07
+P05	1911	8.01	52.8	1.88	2.06	51.74
+P06	2083	7.87	51.32	2.4	1.85	48.44
+P07	2465	4.52	23.85	11.03	2.38	67.92
+P08	2061	6.89	43.81	3.93	2.19	57.17
+P09	2394	8.75	56.27	1.71	1.8	48.47
+P10	2095	8.88	59	1.53	2.14	56.81
+P11	2744	8.51	57.14	1.38	2.14	59.91
+P12	2863	8.12	55.4	1.5	1.96	52.69
+P13	2294	8.23	55.32	1.96	2.09	55.48
+P14	2386	7.09	45.52	2.1	2.21	60.22
+P15	1721	8.98	61.13	1.57	2.24	61.47
+P16	2550	6.79	43.37	2.59	2.23	60.22
+P17	2533	7.36	48.28	2.09	2.3	65.8
+P18	2539	8.56	57.74	1.61	2.16	59.73
+P19	2234	7.78	50.31	2.69	1.92	53.58
+P20	2680	8.03	53.66	1.34	2	56.58
+P21	2361	9.24	61.54	0.93	1.99	57.69
+P22	2209	8.39	56.81	1.54	1.74	49.86
+P23	2365	6.57	41.31	4.02	2.1	56.17
+P24	1448	2.74	10.29	26.1	1.98	67.63
diff -r 000000000000 -r 7ecbc3ec2f55 test-data/calc_robust_z.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/calc_robust_z.tabular	Wed Jun 01 03:59:51 2016 -0400
@@ -0,0 +1,385 @@
+#Well	Table_1	Table_2	Table_3	Table_4	Table_5	Table_6
+A01	-0.34	-0.25	-0.6	1.31	1.38	0.61
+A02	1.15	-0.44	-0.42	-0.42	-1	-0.73
+A03	-0.31	1.18	0.93	-1.03	0.03	0.66
+A04	0.44	0.07	0.02	0.26	-0.7	0.27
+A05	-1.31	1.8	1.28	-0.89	-0.35	0.66
+A06	-0.03	-0.39	-0.3	-0.42	-1.43	-0.82
+A07	-0.29	0.31	0.21	-0.42	-0.22	0.5
+A08	0.28	-0.53	-0.41	-0.43	-0.89	-0.39
+A09	1.1	0.17	0.15	0.25	0.32	0.76
+A10	1.1	-0.04	-0.07	0.54	-0.05	0.16
+A11	0.49	0.18	0.04	-0.12	1.08	1.12
+A12	0.7	0.15	-0.05	0.76	0.05	0.05
+A13	-1.74	1.76	1.02	-0.67	-0.27	0.01
+A14	0.74	-0.67	-0.96	0.82	-0.08	0.09
+A15	-0.13	1.55	1.11	-1	0.76	1.26
+A16	-0.8	1.69	1.06	-0.8	0.7	1.5
+A17	-0.57	0.36	0.26	-0.35	0.13	0.81
+A18	0.28	-0.08	-0.18	0.46	-0.27	0.47
+A19	-0.19	-0.39	-0.37	-0.54	-0.22	-0.19
+A20	-0.17	0.94	0.95	-0.85	-1.13	-0.56
+A21	0.15	0.85	0.87	-1.12	-0.89	-0.13
+A22	-2.55	1.01	0.85	-0.87	-1.16	-0.89
+A23	-0.26	0.43	0.5	-1.19	-0.62	-0.47
+A24	-0.78	-0.77	-0.84	-0.02	-0.92	-0.15
+B01	-0.42	0.73	0.4	-0.65	-0.19	0.05
+B02	-0.62	0.06	-0.36	1.91	0.11	0.65
+B03	-1.78	1.29	0.86	-1.02	-1	-0.38
+B04	0.29	0.41	0.3	-0.77	-1	-0.33
+B05	-1.33	1.72	1.43	-0.89	-1.16	-0.24
+B06	-1.46	-0.12	-0.42	1.15	-0.3	-0.23
+B07	-1.74	2.04	1.48	-0.96	-0.7	0.31
+B08	-0.38	0.54	0.74	-0.81	0.08	0.15
+B09	-0.77	-0.35	-0.24	-0.25	-1.19	-1.23
+B10	-2.56	1.62	1.21	-0.87	-0.97	-1.13
+B11	0.46	-1.34	-1.48	2.76	1.65	2.05
+B12	0.9	0.04	0.06	0.72	0.24	0.3
+B13	-1.32	1.09	0.73	0.12	0.13	0.72
+B14	0.92	-1.08	-1.2	2.97	0.38	0.83
+B15	0.23	0.79	0.77	-0.48	0.65	1.7
+B16	-0.72	1.77	1.62	-1.2	0.35	1.39
+B17	-0.66	1.09	0.96	-0.94	-0.49	0.2
+B18	0.95	0.76	0.93	-0.72	-0.03	0.6
+B19	-0.18	-0.8	-0.73	-0.34	-1.13	-0.91
+B20	0.05	2.15	1.74	-1.37	-0.46	0.57
+B21	-0.59	0.85	1.08	-0.67	-0.22	0.16
+B22	0.01	0.41	0.55	-0.82	-0.97	-0.62
+B23	-2.99	1.72	1.11	-1.25	-0.13	-0.57
+B24	-1.76	-1.21	-1.16	0.44	-0.78	-0.61
+C01	0.01	0.29	0.31	-0.48	-0.89	-0.89
+C02	0.82	0.7	0.64	-0.71	-1	-0.97
+C03	-0.11	-0.51	-0.57	0.14	-1.43	-1.34
+C04	0.4	0.21	0.22	-0.5	-1.03	-1.18
+C05	0.75	0.67	0.68	-1.31	-1.21	-1.07
+C06	1.42	0.35	0.37	-0.86	-0.51	-0.56
+C07	0.67	-0.67	-0.62	-0.2	0.05	-0.24
+C08	0.76	0.21	0.4	-0.4	0.32	0.3
+C09	1.2	-0.56	-0.41	-0.11	-0.51	-0.71
+C10	1.32	0.16	0.35	-0.13	0.51	0.49
+C11	0.23	0.36	0.41	0.04	-0.05	0.16
+C12	1.3	-1.48	-1.48	2.6	1.27	1.46
+C13	2.13	-0.16	-0.15	0.33	0.08	0.56
+C14	0.67	-0.43	-0.41	0.77	1.43	2.03
+C15	0.91	-0.3	-0.27	-0.29	0.16	0.58
+C16	0.16	1.01	1	-1.27	0.59	1.11
+C17	1.36	-0.74	-0.54	0.1	1.08	1
+C18	0.8	0.39	0.54	-0.88	-0.38	-0.08
+C19	-0.2	1.07	1.07	-0.74	-0.81	-0.26
+C20	-0.47	0.12	0.21	-0.27	1.05	0.69
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+N12	0.85	0	0.1	-0.8	-0.35	-0.81
+N13	0.51	-0.59	-0.73	1.32	0.78	0.52
+N14	0.92	-1.73	-1.91	2.29	0.62	-0.1
+N15	-1.4	0.9	0.9	-0.76	0.27	-0.01
+N16	0.02	0.58	0.75	-0.63	-0.05	-0.03
+N17	-1.24	1.42	1.28	-0.91	-0.38	-0.17
+N18	1.41	-0.12	0.04	-0.31	0.08	-0.14
+N19	1.06	-0.25	-0.17	0.59	0.81	0.72
+N20	-0.27	-1.09	-1.06	1.84	0.57	0.08
+N21	0.64	-2.1	-2.36	4.1	0.35	0.26
+N22	-1.86	0.61	0.54	-0.5	0.46	0.34
+N23	0.49	0.59	0.82	-0.71	-0.27	-0.22
+N24	-1.17	-0.46	-0.36	0.49	0.05	0.45
+O01	-0.35	-0.88	-1.17	3.93	0.3	0.33
+O02	-0.9	0.94	0.49	0.78	-1.16	-1.23
+O03	-0.56	0.05	-0.2	2.46	-0.46	-0.49
+O04	-0.35	1.41	1.05	-0.61	-0.86	-0.76
+O05	0.77	-0.09	-0.01	-0.13	-1.48	-1.66
+O06	0.71	-0.56	-0.66	2.02	-0.22	-0.29
+O07	0.91	-0.14	-0.24	0.34	-0.89	-1.04
+O08	0.07	-0.45	-0.33	-0.05	-0.86	-1.5
+O09	0.77	-0.1	-0.1	-0.05	-0.78	-1.26
+O10	1.01	0.14	0.23	0.19	-0.65	-1.07
+O11	0.23	0.67	0.52	-0.14	-0.7	-0.8
+O12	-0.5	1	0.78	-0.42	-1.13	-1.3
+O13	-1.25	0.15	-0.12	0.65	-0.78	-0.78
+O14	0.13	0.94	0.74	-0.88	-0.4	-0.13
+O15	0.1	0.75	0.89	-0.26	0.05	0.48
+O16	0.48	0.32	0.13	-0.02	-0.46	-0.53
+O17	-0.35	-0.09	-0.09	-0.29	-0.59	-0.56
+O18	-0.17	-0.42	-0.43	1.53	0.27	-0.12
+O19	0.09	0.08	0.21	-0.25	-1.46	-1.41
+O20	-1.25	-0.21	-0.17	-0.22	-1.27	-1.55
+O21	0.12	-0.47	-0.48	0.99	-0.54	-0.45
+O22	0.16	0.19	0.26	-0.12	-0.27	-0.45
+O23	0.71	-0.56	-0.6	0.88	-0.35	-0.61
+O24	-0.59	-1.9	-2.18	3.42	0.76	0.51
+P01	-1.91	-3.27	-3.81	12.86	1.05	1.28
+P02	-0.45	-2.51	-2.97	5.52	-1.05	-1.66
+P03	-1.07	-1.36	-1.39	1.64	-1.75	-2.1
+P04	-0.4	-0.92	-1.12	1.46	-1.56	-1.8
+P05	-1.1	-0.85	-0.89	0.51	-0.92	-1.74
+P06	-0.67	-0.95	-1.04	1.11	-1.48	-2.03
+P07	0.29	-3.26	-3.88	11.06	-0.05	-0.33
+P08	-0.72	-1.62	-1.82	2.88	-0.57	-1.27
+P09	0.11	-0.34	-0.53	0.32	-1.62	-2.03
+P10	-0.64	-0.25	-0.25	0.11	-0.7	-1.3
+P11	0.98	-0.51	-0.44	-0.06	-0.7	-1.03
+P12	1.28	-0.78	-0.62	0.07	-1.19	-1.66
+P13	-0.14	-0.7	-0.63	0.61	-0.84	-1.42
+P14	0.09	-1.49	-1.64	0.77	-0.51	-1
+P15	-1.58	-0.19	-0.03	0.16	-0.43	-0.9
+P16	0.5	-1.69	-1.86	1.33	-0.46	-1
+P17	0.46	-1.3	-1.35	0.76	-0.27	-0.52
+P18	0.47	-0.47	-0.38	0.2	-0.65	-1.05
+P19	-0.29	-1.01	-1.14	1.45	-1.3	-1.58
+P20	0.82	-0.84	-0.8	-0.11	-1.08	-1.32
+P21	0.03	-0.01	0.02	-0.58	-1.11	-1.22
+P22	-0.35	-0.59	-0.47	0.12	-1.78	-1.9
+P23	0.04	-1.84	-2.07	2.98	-0.81	-1.36
+P24	-2.26	-4.48	-5.28	28.44	-1.13	-0.36
diff -r 000000000000 -r 7ecbc3ec2f55 test-data/plate_config.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plate_config.txt	Wed Jun 01 03:59:51 2016 -0400
@@ -0,0 +1,1 @@
+well	type	name	geneID
B02	poscontr	Hamp	57817
C02	negcontr	OTP	-1
D02	poscontr	PLK	5347
E02	poscontr	TOX	-1
F02	negcontr	OTP	-1
G02	poscontr	MPEG1	17476
H02	poscontr	TOX	-1
I02	poscontr	PLK	5347
J02	negcontr	OTP	-1
K02	poscontr	TOX	-1
L02	poscontr	Hamp	57817
M02	negcontr	OTP	-1
N02	poscontr	PLK	5347
O02	negcontr	mock	-1
B23	poscontr	PLK	5347
C23	negcontr	OTP	-1
D23	poscontr	TOX	-1
E23	negcontr	OTP	-1
F23	poscontr	PLK	5347
G23	poscontr	MPEG1	17476
H23	poscontr	TOX	-1
I23	negcontr	OTP	-1
J23	poscontr	PLK	5347
K23	poscontr	Hamp	57817
L23	negcontr	OTP	-1
M23	poscontr	MPEG1	17476
N23	negcontr	OTP	-1
O23	negcontr	mock	-1
\ No newline at end of file