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Answer: replace cat with message in glmTreat when lfc = 0
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Gordon Smyth
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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 …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
How did you make this plot? I've never seen an MDS plot from limma/edgeR with axis scale going from -200 to 200.
Personally, I would go ah…
Comment: readDNAStringSet with non DNA characters
by
biomiha
▴
20
DECIPHER does the trick, thank you!
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
James W. MacDonald
68k
It may not be that common for bulk RNA-Seq, but in my experience it's very common for bulk miRNA-Seq.
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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abaed
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0
Nice. That's great to hear. `sva` was actually the next step I was planning to try. My colleagues haven't seen this kind of pattern before …
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