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Hi all,
I have a study involving multiple treatment groups (A, B, C and D) vs a baseline condition (Z). There are 6 biological replicates in each treatment group. I'm interested in using DESeq or edgeR to compare A vs Z, B vs Z, etc. but also A vs B, B vs C, etc. I've followed the manuals for both packages and have obtained 'one-at-a-time' pairwise comparisons. The edgeR documentation suggests that specifying all columns of the count matrix in the final step will give all possible pairwise comparisons, but I've found it only does columns 2,3,4, or 5 versus column 1.
Does a more experienced user of these packages (I've been working with them for 1 week only!) have a way of doing this?
Thanks in advance for any info.
I have a study involving multiple treatment groups (A, B, C and D) vs a baseline condition (Z). There are 6 biological replicates in each treatment group. I'm interested in using DESeq or edgeR to compare A vs Z, B vs Z, etc. but also A vs B, B vs C, etc. I've followed the manuals for both packages and have obtained 'one-at-a-time' pairwise comparisons. The edgeR documentation suggests that specifying all columns of the count matrix in the final step will give all possible pairwise comparisons, but I've found it only does columns 2,3,4, or 5 versus column 1.
Does a more experienced user of these packages (I've been working with them for 1 week only!) have a way of doing this?
Thanks in advance for any info.