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Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Comment: deseq2 lfc shrinkage with few DEGs
by
Michael Love
43k
Agree with your edit.
Votes
A: use tximport's countsFromAbundance when using DESeq2
Comment: Using TPM from tximport of Salmon output for singscore
Answer: Using TPM from tximport of Salmon output for singscore
Comment: deseq2 lfc shrinkage with few DEGs
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
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