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Old 04-28-2016, 05:00 AM   #7
illinu
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Location: US

Join Date: Jul 2013
Posts: 55
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Hi Devon,

Thank you for replying. If I understand correct I should avoid the LRT test? I could use the interaction term like so:
resGenotype <- results(ddsM, contrast=list("conditionTreat.genotypeB")) ??

This arises a new question, if I define my conditions variable as:

Code:
 condition=rep(rep(c("A.ctl","A.treat","B.ctl","B.treat"),each=3),2)
To the question, how do A and B respond differently to the treatment could also be answered like this?

Code:
AB <- DESeqDataSetFromMatrix(countData = countData,colData = colDataAB, design = ~ condition)
ABpairwise <- DESeq(AB)
resAB <- results(ABpairwise, contrast = c("condition", "A.treat", "B.treat"))
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