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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,…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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