[BioC] adjustment for dependent hypotheses when pairwise testing

[pmt1rew@leeds.ac.uk]

Dear all,

I data for 13 genes with the samples from 4 different tissue types.  Would like
to compare the normal means of the different tissue types using pairwise
testing with an adjustment for fdr.

Having considered the Benjamini and Yekutieli reference on the p.adjust help
page I am unsure as to whether my dependency structure satisfies the criteria
to just use the regular "BH" adjustment or if  the "BY" adjustment would be
more appropriate?

Any suggestions for me please?

Many thanks

Rebecca Walls