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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, …
Answer: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
> When I specify lfcThreshold instead of post-hoc LFC filtering, some genes with very low expression and biologically negligible change are…
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