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I am a bit confused with the "lfcshrink" function in DESeq2. I would assume that one would want to use the shrunk result table in subsequent DE gene analysis, but the DESeq2 manual suggests that lfc shrinkage is only used for data visualisation. Could someone clarify how "results" and "lfcshrink" are differentially used in the pipeline?
Thanks for the reply. I now understand why I should use lfcShrink, but wonder whether one can pass all the results arguments in this function as well, e.g. cooksCutoff, independentFiltering, altHypothesis, filterFun. Does lfcShrink run results internally or should I have to run results first and then apply lfcShrink?
If you have specific arguments for results() it's better to use this paradigm below. The "..." in lfcShrink() are passed to external shrinkage methods, not to results(), so you can just run results() with those arguments and pass the `res` object to lfcShrink to add the posterior mode and SD.