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Answer: Rlog performed on tpm or raw transcript abundances?
If you examine the counts in dds, they should correspond to abundance rather than TPM. [eggy car](https://eggycar.co/)
Comment: checkFullRank(modelMatrix) while neither factor can be predicted from each other
Mother 3 might be breaking the whole thing...try omitting her and see if it will run. You might still have issues with certain mothers bei…
Comment: Rlog performed on tpm or raw transcript abundances?
Abundance. If you look at the counts in dds, they should match abundance, not TPM (unless there is a slight shift due to the transcript-le…
Comment: Setting up contrasts within a dataset within conditions (across different genoty
Thanks very much! I'll give that a try.
Answer: question about removing both known and unknown confounders
If my understanding of RUV is correct, I think you should do a LRT in the first DESeq() run (the one that defines `not.sig`). I would use t…
Answer: countToFPKM and featureLength
C: Effect of lfcThreshold on p-value in DESeq2
Comment: SV4Vectors DataFrame bug with haven_labelled data
A: ntop parameter in plotPCA(). DESeq2
Comment: ntop parameter in plotPCA(). DESeq2
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