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
+
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MA plots
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+
Densities plot
+Before NM
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+
+
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+
+
+ Preprocessing microarrays datasets.Contains Background Correction, Normalization within arrays, between arrays (depending on the number of channels) and summarization.
+
+ citations.xml
+
+
+ r-biocmanager
+ pandoc
+ 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
+
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+ 'Read.Project' in value.name
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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 4f7fbd73a770 -r 8aaf6fdb06d6 preprocess_datasets/TwoColors.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_datasets/TwoColors.Rmd Sat Dec 16 12:30:14 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 4f7fbd73a770 -r 8aaf6fdb06d6 preprocess_datasets/look.css
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 4f7fbd73a770 -r 8aaf6fdb06d6 preprocess_datasets/test-data/Matrix.Data.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_datasets/test-data/Matrix.Data.tsv Sat Dec 16 12:30:14 2023 +0000
@@ -0,0 +1,481 @@
+GSM103772_1 GSM103772_2 GSM103773_1 GSM103773_2 GSM103774_1 GSM103774_2 GSM103775_1 GSM103775_2
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+5G10 0.516667375 0.422684187 1.030558370 1.200050245 -0.084552589 0.433503606 -0.739029043 -0.598823231
+5G12 -1.463905057 -1.402083724 -0.086693921 -0.442613756 -0.300188526 0.013501827 -0.647660503 -0.683328685
+5A2 1.983041651 1.890805219 4.157921179 2.417663552 0.541765810 1.187883124 -0.119108337 0.189675327
+5A4 1.861560797 1.976577638 4.000809743 3.155137239 3.132499512 3.349184851 1.789802335 1.793008137
+5A6 0.543458066 0.613999094 1.686044152 1.485605426 1.632757669 2.025063604 1.244786790 1.359382849
+5A8 1.177847097 0.868059055 1.700229313 1.376196350 -0.969329515 -0.239935191 -1.803087805 -1.660314342
+5A10 0.592438126 0.687206504 1.111643069 0.177746697 -0.205772783 -0.096446940 -0.721558025 -0.695915039
+5A12 0.521511011 0.346588933 1.915750244 2.056182912 3.425891956 4.078232707 1.527437141 1.951658153
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+Preprocessing
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+ Preprocessing Plots Before and After
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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
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Preprocessing
+ ++Preprocessing of an extern DataSet, issued from +GenePix_Two_Colors +technology. +
+ +Used methods for each step
+ +Background correction methods
+ +method : auto+ +
Normalization methods
+ +methodNWA : median+ +
methodNBA : quantile+ +
Boxplots
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