# HG changeset patch # User proteomisc # Date 1701532177 0 # Node ID dcfc14781d54d9abd8396d70115101a47f39c712 # Parent cc619066d6f75462d73b0ce49f490eb31a7e18a3 Uploaded diff -r cc619066d6f7 -r dcfc14781d54 preprocess_datasets/Preprocess_DataSet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/preprocess_datasets/Preprocess_DataSet.xml Sat Dec 02 15:49:37 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 + + + + + +