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Answer: Advice needed: Using limma for differential pathway analysis with continuous dis
by
Gordon Smyth
52k
limma has always handled any combination of continuous or categorical variables from the very beginning. You simply add continuous variable…
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
•
0
Hi @yangliao, thanks for the note.
We use Feature Counts extensively for gene-level counting (exon features).
Unfortunately though, and I…
Comment: Feature Counts - potential bug with outfile.jcounts
by
Yang Liao
▴
450
When you use `featureCounts` to count junctions with the `-J` option, it doesn't check if the junction is exactly overlap with exons of gen…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
ATpoint
★
4.6k
I think you run into the common pitfall that you treat results as categorical (significant, not significant) whereas in reality the results…
Comment: DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMe
by
swbarnes2
★
1.4k
It would probably help if you broke out the raw and normalized read counts for all the samples.
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