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updated 22 months ago by
Michael Love
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written 22 months ago by
vincent.croset
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updated 16 months ago by
Aaron Lun
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written 16 months ago by
Peter Hickey
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Answer: Question on RNA-Seq single sample data analysis in EdgeR
by
Gordon Smyth
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Yes, it is necessary to run `calcNormFactors`, as it always is for any DE analysis.
edgeR computes logCPM from all the samples. Computin…
Comment: How to run GSVA with partially NA genes
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blakebowen
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I was a little worried about discarding so many genes, although sounds like this can't be helped. The results are still quite useful so I t…
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Ali Barry
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Thanks, I'll trying playing a bit there. I have done some minor filtering already (requiring at least 5 counts in 10% of my samples, across…
Comment: ashr vs apeglm for interaction data
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Michael Love
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I see why apeglm is conservative— the dispersion is very high within group.
An idea would be to use ashr but do some additional filtering …
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ATpoint
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That’s an Excel problem, not a GEO/R problem or related to limma and Bioconductor.
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