Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ
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harelarik ▴ 60
@harelarik-13564
Last seen 2.4 years ago
Israel

Just joined the forum.

 

Thank you,

 

A

LIMMA VST • 2.1k 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 7 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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