I encountered with inconsistency while using
lfcShrink and I would like to consult with you.
There is option to use
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?