Entering edit mode
Hi,
I have sample information (sampleinfo) in this format:
SampleID condition type
MP_1 A_1 Paired-End
MP_2 A_1 Paired-End
MP_3 A_1 Paired-End
MN_1 A_2 Paired-End
MN_2 A_2 Paired-End
MN_3 A_2 Paired-End
WP_1 B_1 Paired-End
WP_2 B_1 Paired-End
WP_3 B_1 Paired-End
WN_1 B_2 Paired-End
WN_2 B_2 Paired-End
WN_3 B_2 Paired-End
I want to compare A1 with A2, B1 with B2 ans also want to compare (A1+A2) with (B1+B2).
This is how I used DESeqDataSetFromMatrix
ddsMat <- DESeqDataSetFromMatrix(countData = seqdata[,rownames(sampleinfo)], colData = sampleinfo, design = ~ condition)
ddsMat <- DESeq(ddsMat)
res.05_FC0<-results(ddsMat,contrast = c("condition","A_1","A_2"),alpha=0.05,lfcThreshold = 0)
res.05_FC0<-results(ddsMat,contrast = c("condition","B_1","B_2"),alpha=0.05,lfcThreshold = 0)
How can I compare (A_1+A_2) with (B_1+B_2) using the contrast argument in results function?
Hi Michael, I read the examples, I am getting this as my output to
resultsNames(ddsMat)Do I need to use contrast in a list fashion, something like this to capture(A1+A2) vs (B1+B2)
and keep the listValues as default. Would that be correct? Of course it is a little confusing and I can actually make another sampleinfo table, but I want to learn how it will be done here. Thanks
Can you look over this related thread for more background:
https://support.bioconductor.org/p/117940/#126943