[BioC] phenoTest and variable-wise multiple testing

[Jon Manning]

Hi Bioconductors,

I'm using the phenoTest package to look for associations between various 
continuous and categorical clinical variables and methylation values 
stored in an eset-like object.

As suggested I apply the BH method to correct for multiple testing 
probe-wise. However, as I understand it this does not account for 
variable-wise multiple testing, and with my collaborator introducing 
many new variables I'm concerned this will create unnecessary spurious 
associations.

So the question is simple: should I just do a simple column 
(variable)-wise bonferroni correction, after the row (probe) -wise BH 
correction?

All pointers appreciated,

Regards,

Jon Manning

-- 
Dr Jonathan Manning
Bioinformatics Team
Centre for Cardiovascular Science
University of Edinburgh
Queens Medical Research Institute
47 Little France Crescent
Edinburgh  EH16 4TJ
United Kingdom
T: +44 131 242 6700
F: +44 131 242 6782
E: jmanning at staffmail.ed.ac.uk


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.