differentially expressed genes

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)

GenomeMatrix integrates information from diverse experimental data resources for different organisms with respect to user-defined groups of Ensembl genes.