Question: Using limma::roast/camera/romer etc from DESeq2
2
gravatar for phil.chapman
4.1 years ago by
phil.chapman140
United Kingdom
phil.chapman140 wrote:

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

limma edger camera deseq2 romer • 893 views
ADD COMMENTlink modified 4.1 years ago by Gordon Smyth38k • written 4.1 years ago by phil.chapman140
Answer: Using limma::roast/camera/romer etc from DESeq2
2
gravatar for Gordon Smyth
4.1 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

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.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Gordon Smyth38k

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

ADD REPLYlink written 4.1 years ago by phil.chapman140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 164 users visited in the last hour