Using limma::roast/camera/romer etc from DESeq2
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phil.chapman ▴ 150
@philchapman-8324
Last seen 5.9 years ago
United Kingdom

Hi,

I would like to apply the limma gene set tests such as camera, romer etc to my RNAseq dataset which I have analysed in DESeq2.  Am I right in thinking that the rlog transformed counts are the appropriate matrix to pass into these functions?  I can't find a worked example anywhere that integrates these two workflows but apologies if I've missed it.  Within EdgeR there are specific functions to pass a DGEList object to camera (edgeR::camera.DGEList) so I suppose a feature request for DESeq2 would be something similar, but certainly some guidance in the documentation on how to do this would also be welcomed!

Again, apologies if I've just missed the obvious.

Thanks,

Phil Chapman

Drug Discovery Unit, Cancer Research UK Manchester Institute

deseq2 edger limma romer camera • 1.6k views
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@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia

Passing rlog transformed counts to limma may work ok.

edgeR's method of accessing the limma functions is however different and specific to the NB modeling context.

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Thanks.  I'll make a DGEList object in edgeR for now and experiment with that.

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