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Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
andrebolerbarros
▴
10
Hi Michael,
I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
36k
So the way the p-values are generated (non-parametric) you won't get a ranking among these that are highly significant. You can use logFC. …
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
Michael Love
36k
Note sure why it's having difficulty converging.
You could use apeglm?
Comment: performing the differential binding in ChIP-seq
by
ATpoint
★
1.2k
Cross-posted https://www.biostars.org/p/9524012/#9524012
Comment: Transcript-level differential expression using DESeq2
by
Ekta
•
0
Yes, i tried that. I used salmon bootstraps also for the same RNAseq data to run Swish and performed the Differential transcript expressio…
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