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I encountered with inconsistency while using lfcShrink and I would like to consult with you.
There is option to use contrast or coef parameters with this function. contrast can receive a list of 2 character vectors, while coef can receive only elements of resultsNames(dds). This is issue for me because with contrast switch between the elements affect the sign of log2foldchange, and with coef I can't control it.
Do you have solution for this issue?
Can you point out to this discussion? I can't find answer for this issue there
For all Bioconductor packages, not only DESeq2, you can either find these on the package homepage, or you can directly type into your R console:
vignette(“DESeq2”)
Yes I know, but I can't find anything there regarding the problem I mentioned here
Extended section on shrinkage (or something like this) should be a header in the table if contents. You can search for “Extended section”