Preprocessing
++Preprocessing of an `r datasetsource` DataSet, issued from +`r technology` +technology. +
+Used methods for each step
+ +Background correction methods
+method : `r listArguments[["backgroundcorrection_method"]]`+
Normalization methods
+method : `r listArguments[["normalization_method"]]`+
Summarization methods
+method : `r listArguments[["summary_method"]]`+
Boxplots
+Before NM
+
+
+
+
+
After NM
+
+
+
+
+
MA plots
+
+
+
+
+
Densities plot
+Before NM
+
+
+
+
+
After NM
+
+
+
+
+
+
+ Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization.
+
+ citations.xml
+
+
+ r-base
+ r-batch
+ bioconductor-affyplm
+ bioconductor-affy
+ bioconductor-annotate
+ r-knitr
+ bioconductor-marray
+ r-idpmisc
+ r-kernsmooth
+ r-rmarkdown
+ r-markdown
+ bioconductor-limma
+ r-idpmisc
+
+
+
+
+
+
+
+
+ 'Read.Project' in value.name
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**Authors** T.Bensellak, B.Ettetuani.
+
+---------------------------------------------------
+
+==================================
+Preprocessing Microarray DataSet
+==================================
+
+-----------
+Description
+-----------
+
+This tool is used as first phase of the global workflow, the preprocessing .
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
++-------------------------------+------------------------------+---------+
+| Name | output file |format |
++===============================+==============================+=========+
+| Read.DataSet.Microarray | MicroArrayObject.RData | Rdat |
++-------------------------------+------------------------------+---------+
+
+
+**Downstream tools**
+
++-----------------------------------------------+----------------------------------------------+---------+
+| Name | Output file | Format |
++===============================================+==============================================+=========+
+|Tests and Selection | Test.results.tsv | Tabular |
++-----------------------------------------------+----------------------------------------------+---------+
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| Parameter : num + label | Format |
++===========================+============+
+| Image | Rdata |
++---------------------------+------------+
+| Methods parmeters | Numeric |
++---------------------------+------------+
+
+------------
+Output files
+------------
+
+**Microarray.Preprocessing.RData**
+
+**Matrix.Data.tsv**
+
+------------------------------
+General schema of the workflow
+------------------------------
+
+https://bensellak.github.io/microarrays-galaxy/workflow.png
+
+
+
+
+
+
diff -r 09a8947f1031 -r bdc430a41508 preprocess_datasets/TwoColors.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_datasets/TwoColors.Rmd Sun Dec 03 14:07:23 2023 +0000
@@ -0,0 +1,387 @@
+
+
+ Preprocessing Plots Before and After
+
+
+
+
Preprocessing
++Preprocessing of an `r datasetsource` DataSet, issued from +`r technology` +technology. +
+Used methods for each step
+ +Background correction methods
+method : `r listArguments[["methodBC"]]`+
Normalization methods
+method : `r listArguments[["methodNBA"]]`+
Boxplots
+Before BG
+
+
+
+
+
After NBA
+
+
+
+
+
Densities plot
+Before BG
+
+
+
+
+
After BG and NBA
+
+
+
+
+
+
+
+
+
+
+ 1.0
+
+
+
+ @Manual{,
+ title = {R: A Language and Environment for Statistical Computing},
+ author = {{R Core Team}},
+ organization = {R Foundation for Statistical Computing},
+ address = {Vienna, Austria},
+ year = {2017},
+ url = {https://www.R-project.org/},
+ }
+
+
+ @Article{,
+ title = {Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in {R} with {batch}},
+ author = {Thomas J. Hoffmann},
+ journal = {Journal of Statistical Software, Code Snippets},
+ year = {2011},
+ volume = {39},
+ number = {1},
+ pages = {1--11},
+ url = {http://www.jstatsoft.org/v39/c01/},
+ }
+
+
+ @Article{,
+ author = {Laurent Gautier and Leslie Cope and Benjamin M. Bolstad and Rafael A. Irizarry},
+ title = {affy---analysis of Affymetrix GeneChip data at the probe level},
+ journal = {Bioinformatics},
+ volume = {20},
+ number = {3},
+ year = {2004},
+ issn = {1367-4803},
+ pages = {307--315},
+ doi = {10.1093/bioinformatics/btg405},
+ publisher = {Oxford University Press},
+ address = {Oxford, UK},
+ }
+
+
+ @Article{,
+ author = {Matthew E Ritchie and Belinda Phipson and Di Wu and Yifang Hu and Charity W Law and Wei Shi and Gordon K Smyth},
+ title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
+ journal = {Nucleic Acids Research},
+ year = {2015},
+ volume = {43},
+ number = {7},
+ pages = {e47},
+ }
+
+
+ @Article{,
+ title = {Quality assessment for short oligonucleotide arrays.},
+ author = {Julia Brettschneider and Francois Collin and Benjamin M Bolstad and Terence P Speed},
+ journal = {Technometrics},
+ year = {2007},
+ volume = {In press},
+ }
+
+
+ @Manual{,
+ title = {annotate: Annotation for microarrays},
+ author = {R. Gentleman},
+ year = {2017},
+ note = {R package version 1.56.0},
+ }
+
+
+ @Manual{,
+ title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+ author = {Yihui Xie},
+ year = {2017},
+ note = {R package version 1.16},
+ url = {http://yihui.name/knitr/},
+ }
+
+
+ @Manual{,
+ title = {marray: Exploratory analysis for two-color spotted microarray data},
+ author = {Yee Hwa Yang with contributions from Agnes Paquet and Sandrine Dudoit.},
+ year = {2009},
+ note = {R package version 1.58.0},
+ url = {http://www.maths.usyd.edu.au/u/jeany/},
+ }
+
+
+ @Manual{,
+ title = {IDPmisc: Utilities of Institute of Data Analyses and Process Design
+(www.idp.zhaw.ch)},
+ author = {Rene Locher and Andreas Ruckstuhl et al.},
+ year = {2012},
+ note = {R package version 1.1.17},
+ url = {https://CRAN.R-project.org/package=IDPmisc},
+ }
+
+
+ @Manual{,
+ title = {KernSmooth: Functions for Kernel Smoothing Supporting Wand and Jones (1995)},
+ author = {Matt Wand},
+ year = {2015},
+ note = {R package version 2.23-15},
+ url = {https://CRAN.R-project.org/package=KernSmooth},
+ }
+
+
+
+
+
+
+
+
diff -r 09a8947f1031 -r bdc430a41508 preprocess_datasets/look.css
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_datasets/look.css Sun Dec 03 14:07:23 2023 +0000
@@ -0,0 +1,317 @@
+/* css racine */
+
+body {
+/* font-family: Comic Sans MS;*/
+}
+
+div.research {
+ background-color: #33ffff; /*#208090 */ /*#228491*/;
+ color: #0000ff; /* ffffff */
+}
+
+div.ensg {
+ background-color: #bbee00;
+ color: #0000ff;
+}
+
+div.research span.invisible {
+ visibility:hidden;
+}
+
+kbd {
+ color: #000000;
+}
+
+pre {
+ color: #000000;
+}
+
+A:link {
+ color: #0000ee; /*#ffffff;*/
+}
+
+A:active {
+ color: #ff0000; /* #ffffff */
+}
+
+A:hover {
+/* font-size: 2em; */
+ text-decoration: none;
+ color: #0000ee; /* ffffff */
+ background-color: #FFFF33;
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+
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+ color: #FF0000;
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+
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+ color: #FF0000;
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+
+div.correction {
+ color: #008800;
+/* color: #000000; */
+}
+
+div.detail {
+ font-size: 70%;
+}
+
+div.section {
+ text-align: center;
+ font-size: 140%;
+ color: #FF0000;
+}
+
+div.subsection {
+ text-align: left;
+ font-size: 120%;
+ color: #bb0000;
+ background-color: #FFFF33;
+}
+
+div.titreDuModule {
+ text-align: center;
+ font-size: 200%;
+ color: #FF0099;
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+
+div.formation {
+ text-align: center;
+ font-size: 120%;
+ color: #FF0099;
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+ text-align: center;
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+ text-align: center;
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+ font-size: 400%;
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+
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+ text-decoration: none;
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+
+div.theoreme:before {
+ content: "Théorème : ";
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+
+div.theoreme:after {
+ content: "emèroéhT";
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+
+div.theoreme ul li:before {
+ content: "1 alinéa ";
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+
+div.theoreme li:after {
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+div.tpR span.detail {
+ font-size: 75%;
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+div.tpR div.correction:before {
+ content: "Idée de la correction : ";
+}
+
+div.tpR div.correction {
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+ border: solid #009999;
+ padding: 0.5em;
+ margin-left: 2em;
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+ border: solid #00cc00;
+ padding: 0.5em;
+ margin-left: 2em;
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+
+div.tpR div.solution:before {
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+div.tpR div.solution {
+ background-color: #ff00ff;
+ border: solid #990099;
+ padding: 0.5em;
+ margin-left: 2em;
+ border-width: 1px;
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+
+div.tpR div.exercice:before {
+ content: "Exercice : ";
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+div.tpR div.exercice {
+ background-color: #00ee00;
+ border: solid #00cc00;
+ padding: 0.5em;
+ margin-left: 2em;
+ border-width: 1px;
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+
+div.tpR div.questions:before {
+ content: "Questions : ";
+}
+div.tpR div.questions {
+ background-color: #ff99ff;
+ border: solid #ff99ff;
+ padding: 0.5em;
+ margin-left: 2em;
+ border-width: 1px;
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+
+div.tpR span.index {
+/* background-color: #ffff33;*/
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+
+div.tpR h1 {
+ font-family: sans-serif;
+ color: #000;
+ border-style: solid;
+ background-color: #ddf;
+ border-color: #88f;
+ border-width: 1px;
+ padding-left: 0.5em;
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+
+div.tpR h2 {
+ font-family: sans-serif;
+ color: #000;
+ border-style: solid;
+ border-color: #8f8;
+ background-color: #dfd;
+ border-width: 1px;
+ padding-left: 0.5em;
+}
+
+div.tpR h3 {
+ font-family: sans-serif;
+ color: #000;
+ border-style: solid;
+ background-color: #fdd;
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+ border-width: 1px;
+ padding-left: 0.5em;
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+
+div.tpR a:link {
+ color: #00f
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+ color: #f0f
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+ margin-left: 1em;
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+ background-color: #eee;
+ border: solid #ccc;
+ padding: 0.5em;
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+ color: #ff0000;
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+ padding-bottom: 1px;
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+
+div.pp {
+ color: #FF0000;
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+
+div.infobulle{
+ position: absolute;
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+ border: 1px solid Black;
+ padding: 10px;
+ font-family: Verdana, Arial;
+ font-size: 13px;
+ background-color: #ffffff;
+ -moz-border-radius: 20px; /* pour avoir des coins arrondis */
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+
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+ background-color: #77ff33;
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+ border-radius: 3em 1em; /* 20px; pour avoir des coins arrondis */
+}
diff -r 09a8947f1031 -r bdc430a41508 preprocess_datasets/preprocess_datasets/Affymetrix.Rmd
--- a/preprocess_datasets/preprocess_datasets/Affymetrix.Rmd Sun Dec 03 14:06:08 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,373 +0,0 @@
-
-
- Preprocessing Plots Before and After
-
-
-
-
Preprocessing
++Preprocessing of an `r datasetsource` DataSet, issued from +`r technology` +technology. +
+Used methods for each step
+ +Background correction methods
+method : `r listArguments[["methodBC"]]`+
Normalization methods
+methodNWA : `r listArguments[["methodNWA"]]`+
methodNBA : `r listArguments[["methodNBA"]]`+
Boxplots
+Before BG
+
+
+
+
+
After BG, NWA and NBA
+
+
+
+
+
+
+
+
+
+
+
+
+
MA plots
+
+
+
+
+
Densities plot
+Before BG
+
+
+
+
+
After BG and NWA
+
+
+
+
+
+
+
+
+
-Preprocessing Plots Before and After
-
-
-
-
Preprocessing
--Preprocessing of an `r datasetsource` DataSet, issued from -`r technology` -technology. -
-Used methods for each step
- -Background correction methods
-method : `r listArguments[["backgroundcorrection_method"]]`-
Normalization methods
-method : `r listArguments[["normalization_method"]]`-
Summarization methods
-method : `r listArguments[["summary_method"]]`-
Boxplots
-Before NM
-
-
-
-
-
After NM
-
-
-
-
-
MA plots
-
-
-
-
-
Densities plot
-Before NM
-
-
-
-
-
After NM
-
-
-
-
-
-
- Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization.
-
- citations.xml
-
-
- r-base
- r-batch
- bioconductor-affyplm
- bioconductor-affy
- bioconductor-annotate
- r-knitr
- bioconductor-marray
- r-idpmisc
- r-kernsmooth
- r-rmarkdown
- r-markdown
- bioconductor-limma
- r-idpmisc
-
-
-
-
-
-
-
-
- 'Read.Project' in value.name
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
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-
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-
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-
-
-
-
-
-
-
-.. class:: infomark
-
-**Authors** T.Bensellak, B.Ettetuani.
-
----------------------------------------------------
-
-==================================
-Preprocessing Microarray DataSet
-==================================
-
------------
-Description
------------
-
-This tool is used as first phase of the global workflow, the preprocessing .
-
------------------
-Workflow position
------------------
-
-**Upstream tools**
-
-+-------------------------------+------------------------------+---------+
-| Name | output file |format |
-+===============================+==============================+=========+
-| Read.DataSet.Microarray | MicroArrayObject.RData | Rdat |
-+-------------------------------+------------------------------+---------+
-
-
-**Downstream tools**
-
-+-----------------------------------------------+----------------------------------------------+---------+
-| Name | Output file | Format |
-+===============================================+==============================================+=========+
-|Tests and Selection | Test.results.tsv | Tabular |
-+-----------------------------------------------+----------------------------------------------+---------+
-
------------
-Input files
------------
-
-+---------------------------+------------+
-| Parameter : num + label | Format |
-+===========================+============+
-| Image | Rdata |
-+---------------------------+------------+
-| Methods parmeters | Numeric |
-+---------------------------+------------+
-
-------------
-Output files
-------------
-
-**Microarray.Preprocessing.RData**
-
-**Matrix.Data.tsv**
-
-------------------------------
-General schema of the workflow
-------------------------------
-
-https://bensellak.github.io/microarrays-galaxy/workflow.png
-
-
-
-
-
-
diff -r 09a8947f1031 -r bdc430a41508 preprocess_datasets/preprocess_datasets/TwoColors.Rmd
--- a/preprocess_datasets/preprocess_datasets/TwoColors.Rmd Sun Dec 03 14:06:08 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,387 +0,0 @@
-
-
- Preprocessing Plots Before and After
-
-
-
-
Preprocessing
--Preprocessing of an `r datasetsource` DataSet, issued from -`r technology` -technology. -
-Used methods for each step
- -Background correction methods
-method : `r listArguments[["methodBC"]]`-
Normalization methods
-method : `r listArguments[["methodNBA"]]`-
Boxplots
-Before BG
-
-
-
-
-
After NBA
-
-
-
-
-
Densities plot
-Before BG
-
-
-
-
-
After BG and NBA
-
-
-
-
-
-
-
-
-
-
- 1.0
-
-
-
- @Manual{,
- title = {R: A Language and Environment for Statistical Computing},
- author = {{R Core Team}},
- organization = {R Foundation for Statistical Computing},
- address = {Vienna, Austria},
- year = {2017},
- url = {https://www.R-project.org/},
- }
-
-
- @Article{,
- title = {Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in {R} with {batch}},
- author = {Thomas J. Hoffmann},
- journal = {Journal of Statistical Software, Code Snippets},
- year = {2011},
- volume = {39},
- number = {1},
- pages = {1--11},
- url = {http://www.jstatsoft.org/v39/c01/},
- }
-
-
- @Article{,
- author = {Laurent Gautier and Leslie Cope and Benjamin M. Bolstad and Rafael A. Irizarry},
- title = {affy---analysis of Affymetrix GeneChip data at the probe level},
- journal = {Bioinformatics},
- volume = {20},
- number = {3},
- year = {2004},
- issn = {1367-4803},
- pages = {307--315},
- doi = {10.1093/bioinformatics/btg405},
- publisher = {Oxford University Press},
- address = {Oxford, UK},
- }
-
-
- @Article{,
- author = {Matthew E Ritchie and Belinda Phipson and Di Wu and Yifang Hu and Charity W Law and Wei Shi and Gordon K Smyth},
- title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
- journal = {Nucleic Acids Research},
- year = {2015},
- volume = {43},
- number = {7},
- pages = {e47},
- }
-
-
- @Article{,
- title = {Quality assessment for short oligonucleotide arrays.},
- author = {Julia Brettschneider and Francois Collin and Benjamin M Bolstad and Terence P Speed},
- journal = {Technometrics},
- year = {2007},
- volume = {In press},
- }
-
-
- @Manual{,
- title = {annotate: Annotation for microarrays},
- author = {R. Gentleman},
- year = {2017},
- note = {R package version 1.56.0},
- }
-
-
- @Manual{,
- title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
- author = {Yihui Xie},
- year = {2017},
- note = {R package version 1.16},
- url = {http://yihui.name/knitr/},
- }
-
-
- @Manual{,
- title = {marray: Exploratory analysis for two-color spotted microarray data},
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- url = {http://www.maths.usyd.edu.au/u/jeany/},
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diff -r 09a8947f1031 -r bdc430a41508 preprocess_datasets/preprocess_datasets/look.css
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diff -r 09a8947f1031 -r bdc430a41508 preprocess_datasets/preprocess_datasets/test-data/Matrix.Data.tsv
--- a/preprocess_datasets/preprocess_datasets/test-data/Matrix.Data.tsv Sun Dec 03 14:06:08 2023 +0000
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Preprocessing
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Densities plot
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