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Answer: Highly DE genes but small count difference within conditions
by
Sadie
• 0
The observation of highly DE (differentially expressed) genes, despite a small count difference within conditions, highlights the complexit…
Comment: GSVA ssGSEA vs. Broad implementation of ssGSEA
by
Bob
▴ 10
Thanks for the prompt answer! I looked into the "original ssGSEA R-implementation" ([https://github.com/GSEA-MSigDB/ssGSEA-gpmodule][1]), u…
Comment: RNASeq Time Course Question
by
jihoon.kim.1495
▴ 10
I see. You'd mean clustering using only the right 5 columns (in the above example), right?
Comment: RNASeq Time Course Question
by
Michael Love
42k
Yes. If you wanted to focus on differences, you could cluster on the subset of coefficients representing differences (interactions).
Comment: RNASeq Time Course Question
by
jihoon.kim.1495
▴ 10
Thanks for the clarification. With regards to your last comment about the clustering by the coefficients/log2fold changes, I wanted to cl…
Votes
C: Vertical line at A=0, nothing else, on MA plot
Comment: RNASeq Time Course Question
Answer: RNASeq Time Course Question
Comment: limma plotMDS - logFC inverted?
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
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