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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
•
0
Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…
Answer: GO.db and others package Download failure
by
James W. MacDonald
68k
You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
MDS of what quantity? LogCPM from `cpm()`?
I don't have a definitive answer, but my feeling that is that library size effects are to be ex…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
•
0
Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…
Answer: replace cat with message in glmTreat when lfc = 0
by
Gordon Smyth
53k
Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …
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