[BioC] multiple comparisons followed by multiple tests

[Matthew Hannah]

I would look at the Limma help pages as this allows Lm fitting and the
specification of multiple comparisons and also P value correction by fdr
(although I think this is only after ebayes mod of t-stats?).

As for the replication if you have less than 3 reps per treatment then
you are obviously wasting your time. Also if they are just technical reps
rather than true biological reps then any statistical analysis will be
misleading due to the underestimate of biological variability. You also
don't mention what type of data (affy or cDNA) or the general design 
which may allow people to offer more detailed advice.

You also don't mention the starting point data - for example if it's affy
data are the signal values from MAS5 or have you looked into using RMA or 
GCRMA as a low-level normalisation?

HTH,
Matt