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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.
Comment: p-adjusted values in multiple comparisons
by
Josh
•
0
Yes, using lmFit with block and duplicateCorrelation is appropriate; mobile data collection can illustrate blocking importance. First estim…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
•
0
Understood, thanks. The issue I'm seeing is that even after normalization, the MDSplot still orders samples by library size. I suspect cell…
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