contrast file in DESeq2 bioconductor
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11 weeks ago
r.shiasi3897 ▴ 10

Hi everyone, I have 3 time points and want to do deseq2 for comparing these 3 time points: is it correct to build my contrast file like below?

results(dds, contrast = c("timepoints", "TS","EOT", "FU"))

I can also take TS (Therapy start) as control and compare EOT (End of treatments) and FU (follow up) as treatment.

DEseq2 • 317 views
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Entering edit mode
11 weeks ago
ATpoint 80k

What do you want to compare?

1) You can compare pairwise, like TS vs EOT and TS vs FU and EOT vs FU.

That would be

results(dds, contrast = c("timepoints", "TS", "EOT"))`

2) You can compare one group versus the average of the other two. For example, TS versus the average of EOT and FU would be something like:

results(dds, contrast = list("TS ", c("EOT ","FU ")), listValues=c(1, -1/2))

The exact syntax depends on how resultsNames(dds) looks, see ?results and also https://support.bioconductor.org/p/69104/ to get that right.

3) You can use the LRT (See vignette of DESeq2) to find any differences between groups, though I personally would only do that with many more than three groups. Pairwise comparisons are probably what you want here.

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Thank you very much. i will try it

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