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Question: Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
0
gravatar for harelarik
4 months ago by
harelarik0
harelarik0 wrote:

Just joined the forum.

 

Thank you,

 

A

ADD COMMENTlink modified 22 days ago • written 4 months ago by harelarik0

There is no Bioconductor package called DSEQ. Do you possibly mean DESeq?

ADD REPLYlink written 4 months ago by Gordon Smyth32k

Yes.

ADD REPLYlink written 22 days ago by harelarik0

Sorry for the late response..

Thank you very much!!!

ADD REPLYlink written 22 days ago by harelarik0

I apologize again for the very late response...

ADD REPLYlink written 22 days ago by harelarik0
1
gravatar for Ryan C. Thompson
4 months ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson6.1k wrote:

There is generally no reason to do this. You can either use voom before running limma or run eBayes with trend=TRUE. Either of these methods should give better results than using VST data.

ADD COMMENTlink written 4 months ago by Ryan C. Thompson6.1k
0
gravatar for Gordon Smyth
4 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Yes, limma will accept vst output from DESeq. You should analyze it using the limma-trend pipeline and this should work fine. However, as Ryan has pointed out, limma doesn't require variance stabilized input and using limma's native pipelines is probably better.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Gordon Smyth32k
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