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Answer: Confirm that OpenStats will not be archived (pryr dependency)
by
shepherl
4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Federico Marini
▴
180
Jumping in on this - all this started because we want to "do it right", i.e. avoiding the post-hoc filtering on the logFC (which is still w…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
it looks above like you have a gene with two non-zero count samples.
Also, yes you can use a stricter filter. You cannot estimate the LFC …
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Ahmed Salah
•
0
Thank you very much for your answer.
Actually, this is after pre-filtering
```r
keep <- rowSums(counts(dds) >= 10) >= 3
dds <- dds[keep, …
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