Bioconductor Bionet

Showing : bionet • reset

vote

1.9k

views

bionet network

updated 9.3 years ago by branislav misovic ▴ 120 • written 9.3 years ago by enricoferrero ▴ 680

vote

replies

1.7k

views

bionet network

updated 9.3 years ago by branislav misovic ▴ 120 • written 9.3 years ago by enricoferrero ▴ 680

votes

replies

1.2k

views

BioNet plotModule

9.8 years ago cristina della beffa ▴ 30

vote

replies

1.9k

views

BioNet bioconductor affymetrixchip network analysis

10.5 years ago svlachavas ▴ 840

votes

replies

1.3k

views

Microarray Visualization Network BioNet Microarray Visualization Network BioNet

15.0 years ago Eva Benito Garagorri ▴ 70

5 results • Page 1 of 1

Recent ...

Replies

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 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.