Pathway Enrichment Exercises
I have placed a DESeq result from another study
in data/res2.RData. Analyze the result with each of ORA, FCS and SPIA methods.
How you do that is relatively freeform, but I suggest you start with the scripts ora.R, fcs.R and spia.R
and modify them to suit your needs. But beware! The gene identifiers used are different so make sure AnnotationDbi
gets the right settings to convert what's in res2.RData to ENTREZ identifiers.