[BioC] Westfall and Young "maxT"

[Douglas Grove]

Hi,

I've got a question regarding the Westfall and Young "maxT" procedure
(implemented in Bioconductor package multtest, function mt.maxT).

If one calculates a two sample T-statistic assuming unequal variances
for the groups, then the resultant statistic is only approximately T
and the degrees of freedom are a function of the sample sizes and 
variances.  So the situation is that the distributions of the T
statistics calculated for different "genes" are in general *not* 
identical.  Obviously, if one has a moderately large sample size
the reference distributions for the different "genes" are all
approximately normal and the difference between distributions
is not anything to worry about.  However, if one's sample sizes are 
smallish, then this could be a problem, correct?  

So my questions are: 

(1) is there anything that can be done to adjust for the differences
    between the distributions of the genes (I'm guessing there isn't)?

and

(2) if there is, does the function mt.maxT() in package multtest implement
    such a adjustment

and

(3) if there is not such an adjustment, is it still reasonable to apply this
    procedure to smallish samples and, if yes, is there any *real* justification
    for doing so.


Any help is much appreciated

Thanks,
Doug Grove
Statistical Research Associate
Fred Hutchinson Cancer Research Center