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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. It would also be sensible to filter non-expressed genes…
Comment: How to run GSVA with partially NA genes
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blakebowen
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0
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…
Comment: ashr vs apeglm for interaction data
by
Ali Barry
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30
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
by
Michael Love
37k
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 …
Comment: How to figure out the FC value from Limma
by
ATpoint
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1.2k
That’s an Excel problem, not a GEO/R problem or related to limma and Bioconductor.
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