Thank you very much!!!

Question

Does LIMMA accept as an input "variance Stabilizing Transformation" generated by DSEQ

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harelarik ▴ 60

@harelarik-13564

Last seen 3.1 years ago

Israel

Just joined the forum.

Thank you,

A

LIMMA VST • 2.5k views

ADD COMMENT • link 7.3 years ago • updated 7.1 years ago harelarik ▴ 60

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

ADD REPLY • link 7.3 years ago Gordon Smyth 51k

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Yes.

ADD REPLY • link 7.1 years ago harelarik ▴ 60

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Sorry for the late response..

Thank you very much!!!

ADD REPLY • link 7.1 years ago harelarik ▴ 60

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I apologize again for the very late response...

ADD REPLY • link 7.1 years ago harelarik ▴ 60

score 1 · Answer 1 · 2017-07-23

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Ryan C. Thompson ★ 7.9k

@ryan-c-thompson-5618

Last seen 6 weeks ago

Icahn School of Medicine at Mount Sinai…

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 COMMENT • link 7.3 years ago Ryan C. Thompson ★ 7.9k

score 0 · Answer 2 · 2017-07-23

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Gordon Smyth 51k

@gordon-smyth

Last seen 11 hours 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.

ADD COMMENT • link 7.3 years ago Gordon Smyth 51k