[BioC] RLMM questions

[Amit Bahl]

I have a custom Affy array which allows several applications  
(expression profiling, genotyping, etc...) on a single chip.  I want  
to use RLMM to analyze our genotyping data, but have a couple of  
questions:

1) Instead of normalizing to the scale of the training set (which I  
don't have), does it make sense to normalize all arrays to each other  
using quantile normalization?  If I do this, then instead of using a  
raw file intermediate, I could go from an abatch object directly to  
the norm files (what is the format of these files?).  This is also  
appealing as gtype_cel_to_pq chokes on my CDF file, probably due to  
the mixed design.

2) Once I have norm files, I can create the theta file - but Is there  
a way to do unsupervised classification from the results in the theta  
file (that is, how do I  avoid the internal regions file altogether  
or make a compatible uninformative one)?  Of course, I could always  
define my own conservative decision regions in the unit square.

3) My genotyping probe-sets don't all have 20 PM probes, does RLMM  
explicitly require this?

4) I'm also interested in checking how much the various quartet  
offsets contribute to classification results.  Are the 20 probes in  
the raw or norm file ordered by offset and strand?

-Amit