Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
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harelarik ▴ 50
@harelarik-13564
Last seen 9 months ago

Just joined the forum.

 

Thank you,

 

A

LIMMA VST • 1.1k views
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There is no Bioconductor package called DSEQ. Do you possibly mean DESeq?

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Yes.

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Sorry for the late response..

Thank you very much!!!

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I apologize again for the very late response...

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@ryan-c-thompson-5618
Last seen 13 months ago
Scripps Research, La Jolla, CA

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.

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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

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.

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