Entering edit mode
21 months ago
biotrekker
▴
110
Hello I have three groups A, B, and C I want design to be (1) A vs (B and C) (2) B vs (A and C) and (3) C vs (A and B). However with contrast parameter inside of results from DESeq2, it seems that I can only choose two at a time? What should I do? Thanks
Seeing as how the rest of my pipeline is in DESeq2, and solutions that are provided in this package?
You can pass the contrast matrix into DESeq2 results directly:
result(dds, contrast=contrast.matrix[,'groupBvsAC'])
"Alternatively, a numeric vector of the length of resultsNames(dds) can be provided, for manually specifying the linear combination of terms."
The call to
limma:makeContrasts
simply helps to get the correct numeric vector; but you can create it manually.