[BioC] RMA with few arrays

[Ann Hess]

I am wondering if it is appropriate to compute expression indices with RMA 
for only a small number of arrays (2 or 3).  I have seen in previous posts 
that the expression indices can be identical for some probe sets across 
different arrays when using RMA with few arrays (because of the median 
polish algorithm).  I have observed this for the data in question.  Is is 
appropriate to just remove those probe sets from down stream analysis?  Is 
there a problem with computing RMA for such a small group of arrays?

The data was generated by a scientist interested in comparing three 
treatments.  However, they ran a single replicate of each treatment and 
then reproduced the experiment at a later date.  So, there are a total of 
6 arrays, but they come from two separate experiments.  Currently, they 
are just interested in comparing two of the treatments.

My plan was to run RMA for each of the experiments separately (since I 
don't think it is appropriate to normalize all the arrays together).  Then 
combine the results and use a paired t-test to test for differential gene 
expression for the two treatment groups of interest.

When I tried this approach (using limma and multtest), the results 
actually looked good until I took a closer look at the RMA values and 
noticed the identical expression indices across arrays for some probe 
sets.

Any suggestions would be greatly appreciated.

Ann