DESeq2 - 3 factor levels

Hi, I’m currently analyzing a dataset produced from DESeq2 in Galaxy. I have two factors, each with three factor levels:

Factor 1: Hour (0, 5, 24 hrs) Factor 2: Tissue (A, B, C)

The summary plots and results files only compare two factor levels at a time, i.e. 24 hrs vs 0 hrs, and tissue C vs tissue A. How can I get the results file for other comparisons, such as 5 hrs vs 24 hrs, or tissue B vs tissue A? I know in R, using the “contrast” argument can do this. Is this possible in Galaxy?

Thanks in advance!

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Hi @julsies

To directly use the contrast function, try edgeR or limma instead.

DeSeq2 has this function (partially) batched in the Galaxy wrapped tool version. The parameter is Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor). That said, this probably isn’t what you want, but you can compare it.

Hope that helps!

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That’s even better! Thank you for letting me know!

Hello @jennaj ,

How to do that? Like I have 3 sample types A,B and C how to compare A with B+C similarly B with other two and so on using edgeR? What to put as contrast function?

Thanks in advance!