Hi,

This question regards how various gene set testing methods deal with
pre-filtered (non-specifically) data sets.

Don’t genes in a gene set that did not pass a filter constitute important
evidence “against” that gene set? Not taking them into account when
calculating whatever gene set summary statistic seems wrong (e.g. as
recommended in chapters 13 & 14 of “Bioconductor Case Studies”, if I read
correctly). To put it differently, excluding a gene in the summary statistic
calculation “because it is likely not to be interesting” seems different
than excluding it because it was not on the chip in the first place.
Best,
François Lefebvre

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