Bioconductor Masks

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multiple sequences masks rowmask rownames biostrings

updated 8.0 years ago by Valerie Obenchain ★ 6.8k • written 8.0 years ago by ben.ward ▴ 30

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Answer: EdgeR: Exact test and glmQLFTest produce very different results by Gordon Smyth 48k

Yes, what you see is what is expected. The whole purpose of the edgeR-quasi pipeline is to give more rigorous control of the FDR rate so it…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 48k

Reitering James' answer, there is no reason not to use `voomLmFit` if you were planning to follow `voom` by `lmFit`. The reason why `voomLm…

Answer: EdgeR: Exact test and glmQLFTest produce very different results by James W. MacDonald 64k

You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.

Answer: limma::voom vs edgeR::voomLmFit - when to use? by James W. MacDonald 64k

The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…

Comment: 'Subtracting' counts on basis of Negative control media and water samples by Karthik • 0

I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…

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Comment: Ensembl down???

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