[BioC] limma power question

[Anthony Bosco]

Hi,

I am using limma to analyse an experiment where I am comparing the 
response in stimulated verses un-stimulated cells in individuals with 
and without disease.

When I ask how individuals with or without disease respond 
differently to the stimulus there are no significant genes when the p 
values are adjusted.

I know that there are differences which have been confirmed by 
qRT-PCR ( and can be demonstarted by analysing data using fold change 
only) and these genes have the highest ranked p values in the limma 
analysis (although not significant when adjusted).

I have tried to filter the data set (to the 3000 most variable genes) 
so there are less comparisons being made and the differences are 
still not significant.

I am using hgu133plus2 chips with 3 replicates.


regards


Anthony
-- 
______________________________________________

Anthony Bosco - PhD Student

Institute for Child Health Research
(Company Limited by Guarantee ACN 009 278 755)
Subiaco, Western Australia, 6008

Ph 61 8 9489  , Fax 61 8 9489 7700
email anthonyb at ichr.uwa.edu.au