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James W. MacDonald
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Comment: Transcript-level differential expression using DESeq2
by
Ekta
•
0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish.
thanks
ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
Michael Love
37k
Sorry, I haven't seen this. Maybe try filtering low count genes?
```
keep <- rowSums(counts(dds) >= 10) >= X
dds <- dds[keep,]
# then run …
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this.
Another…
Comment: Transcript-level differential expression using DESeq2
by
Ekta
•
0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
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…
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