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Recent ...
Replies
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
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> When I specify lfcThreshold instead of post-hoc LFC filtering, some genes with very low expression and biologically negligible change are…
Answer: Array weights in dpcDE
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Gordon Smyth
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The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights.
However,…
Answer: lfc shrinkage estimator in DESeq2
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Michael Love
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Try the vignette which has a lot of information on these type of questions.
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