Thread: DESeq problems
View Single Post
Old 10-03-2011, 09:56 AM   #2
kopi-o
Senior Member
 
Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

I think DESeq is a bit out of sync with the documentation/tutorial at the moment. I ran into the same problems as you, but after looking at some help pages and/or the vignette (can't remember which) I ended up using:

cds <- newCountDataSet(data, conds)
cds <- estimateSizeFactors(cds)
cds <- estimateVarianceFunctions(cds)

res <- nbinomTest(cds, "case", "control")

... which seems to work.
kopi-o is offline   Reply With Quote