DEan

[Alejandra Cervera]

deseq2 option currently gives the same output when testing more than one condition. For example when 3 conditions following files are the same and they should not. deseq2_Cond1vsCond2.csv, deseq2_Cond2vsCond3.csv and deseq2_Cond1vsCond3.csv. When using deseq and edgeR the problem seems to not be present (files are different).

[Alejandra Cervera]

This is the code I use for deseq2

  param1 = "~Treatment"
  dds <- DESeqDataSetFromMatrix(countData = counts,colData = colData,design = as.formula(param1))
  dds <- dds[ rowSums(counts(dds)) > 1, ]
  dds <- DESeq(dds) 
  res <- results(dds)
  table.out <- data.frame(ids=rownames(res), as.data.frame(res))
#this next line tells you which conditions are being compared
  optOut1 <- mcols(res)$description[2]
  rld <- rlog(dds, blind=FALSE)
  write.table(assay(rld),file=get.output(cf,'optOut2'),sep="\t")
#i think it will be great to save dds so we can make plots from it
  save(dds, file=get.output(cf,'optOut3'))

[Chiara Facciotto]

Multiple conditions are now correctly evaluated by DESeq2. I also added an array of RData objects that can be used for plotting.