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DESeq2 genes Differential expressed

2.7 years ago Syed Zaheer ▴ 10

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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…

Answer: Array weights in dpcDE by Gordon Smyth 53k

The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…

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