[BioC] Analysis of Affymetrix Mouse Gene 2.0 ST arrays

[Naxerova, Kamila]

Dear all,

I am analyzing a set of Affymetrix Mouse Gene 2.0 ST arrays. I am quite familiar with 3'-biased chips, but this is my first time looking at data from WT arrays. I have a few general questions -- any advice would be appreciated to speed up my learning process.

1) I have already read on this mailing list that the good old affy package does not work well with WT arrays (can anybody point me to any literature on why that is?). So I have installed the oligo and xps packages -- what are the advantages/disadvantages for each? Any opinions on which one is the right "starter kit"?

2) I see with some dread that there seems to be no annotation package for the 2.0 array yet. I have never built my own... any quick bullet points on how I would go about doing that for a WT array?

3) It seems that RMA is also used for normalization of WT arrays, so that part I am comfortable with. But are there any differences in preprocessing between 3' and WT arrays that I should watch out for?

Thanks so much!
Kamila