Bioconductor

No posts found.

0 results • Page 1 of 1

Recent ...

Replies

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…

Votes

Awards • All