AffyDEGFinder

By | September 22, 2011

Given Affymetrix CEL files, AffyDEGfinder finds differentially expressed genes and runs clustering, annotation, and GO and KEGG enrichment analysis for them using R/Bioconductor through Chipster. This workflow consists of the following steps:

  • Normalize the data using rma (normalized.tsv)
  • Run a statistical test on the normalized data using empirical bayes (two-sample.tsv)
  • Perform hierarchical clustering (hc-genes.txt, hc-chips.txt)
  • Write out a heatmap image (heatmap.png)
  • Annotate results (annotations.tsv)
  • Run the term enrichment analysis for KEGG and GO pathways (hypergeo.html)
Name
AffyDEGFinder
Documentation
http://chipster.csc.fi
Protocol
SOAP
WSDL
Endpoint
http://chipster.csc.fi:80/chipster-ws/chipster
Topic
Microarrays
Type
Analysis
Tags
, , , , , ,
Description

Given Affymetrix CEL files, AffyDEGfinder finds differentially expressed genes and runs clustering, annotation, and GO and KEGG enrichment analysis for [...]

Further information

Given Affymetrix CEL files, AffyDEGfinder finds differentially expressed genes and runs clustering, annotation, and GO and KEGG enrichment analysis for them using R/Bioconductor through Chipster. This workflow consists of the following steps:

  • Normalize the data using rma (normalized.tsv)
  • Run a statistical test on the normalized data using empirical bayes (two-sample.tsv)
  • Perform hierarchical clustering (hc-genes.txt, hc-chips.txt)
  • Write out a heatmap image (heatmap.png)
  • Annotate results (annotations.tsv)
  • Run the term enrichment analysis for KEGG and GO pathways (hypergeo.html)
Original source
BioCatalogue

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