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Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
Denise
•
0
In section 9 Time course experiments of the RNA-seq workflow tutorial, it says
```
library("fission")
data("fission")
ddsTC <- DESeqDataSe…
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
by
Michael Love
43k
I pushed 1.48.2 to release, or you can get the latest with `remotes::install_github("thelovelab/DESeq2")`
Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
James W. MacDonald
68k
I think you misunderstand the interpretation of the interaction coefficients. They estimate the interaction of a given time and time A, bet…
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
by
Michael Love
43k
Thanks for pointing this out! I found a bug that the wrong weights matrix was being used when recomputing the SE within results() for the n…
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
by
Michael Love
43k
Is it the case that you are running DESeq2 across 12 total features? This is a larger issue: I wouldn't use an NB model on such counts. The…
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