Hi,

The output of `romer` in `limma` includes a field called "Mixed." The man page defines it as "[...]p-values for the alternative hypotheses mixed[...]", but neither paper cited mention what that alternate hypothesis actually means. Can anyone enlighten me as to what that p-value actually means?

Best regards,
John Ma, PhD
University of Texas MD Anderson Cancer Center

Is your question biological or statistical? If the latter, it seems pretty clear from the help page you reference:

     In the output, p-values are given for each set for three possible
     alternative hypotheses. The alternative "up" means the genes in
     the set tend to be up-regulated, with positive t-statistics. The
     alternative "down" means the genes in the set tend to be
     down-regulated, with negative t-statistics. The alternative
     "mixed" test whether the genes in the set tend to be
     differentially expressed, without regard for direction. In this
     case, the test will be significant if the set contains mostly
     large test statistics, even if some are positive and some are
     negative. The first two alternatives are appropriate if you have a
     prior expection that all the genes in the set will react in the
     same direction. The "mixed" alternative is appropriate if you know
     only that the genes are involved in the relevant pathways, without
     knowing the direction of effect for each gene.

And now, after re-reading it, I would say it pretty well covers the biological interpretation as well. Is there something here that you find unclear?