# HG changeset patch # User proteomisc # Date 1701532028 0 # Node ID 52ccb90adf01869c3691255cbe7ad07d4099c133 # Parent a76041fa13d797c38c596e1f103eb4d5d3a08bf1 Uploaded diff -r a76041fa13d7 -r 52ccb90adf01 Preprocess_DataSet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Preprocess_DataSet.xml Sat Dec 02 15:47:08 2023 +0000 @@ -0,0 +1,306 @@ + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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 + + + + + +