[BioC] Two rma questions

[Simon Kidd]

Hi,

We have been comparing the effects of a mutation to two different 
duplications of the wild type gene (ie  g-  v g-/dp1(g+)  and g-  v 
g-/dp2(g+)) and then doing rma on either the pooled affy chips or the 
two genotypes separately and then pooling them for analysis in dChip. 
But which of the methods, separate or together is the statistically 
the correct way of doing the rma analysis? The two give different 
numbers of differentially expressed genes.

The second question, does rma  in affy v1.4.21 have the same bug as 
justRMA and gcRMA in affy v1.4.22?

thanks,

Simon