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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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Gordon Smyth
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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
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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
by
abaed
•
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 …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
James W. MacDonald
68k
It is not uncommon for library size to be apparent in an MDS plot. You can use `sva` or `RUV` to account for that.
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