[BioC] Selection of quantitative differences b/w two M vs A plots after rma

[Anthony Bosco]

Hi.

In my experiments I have control and stimulated cell cultures for 
individuals with and without disease (usually no replicates, but 
sometimes up to 3 replicates).

Therefore I have two M vs A plots, control verses stimulus for the 
disease group, and control verses stimulus for the group with no 
disease.

For each group, I analyse Affy data with rma and generate M vs A plots.

I define everything with M value > 0.45 (in a 2 chip comparison) as 
differentially expressed, but some genes are differentially expressed 
in the disease and no disease groups, but at a much higher level in 
one of the groups.

Currently since I define the noise as m = 0.45, I just simply 
subtract the m values for any gene which is differentially expressed 
in both M vs A plots, and if the difference is greater than 0.45 I 
call that different between both groups.

1) Is this correct?

2) Does any one know how many false positives to expect in two chip 
comparisons with Affy chips


Regards


Anthony
-- 
______________________________________________

Anthony Bosco - Cell Biology Research Assistant

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