[BioC] Combining Affymetrix miRNA samples from different arrays

[Michal Blazejczyk]

Dear group,

We have a customer who has two datasets obtained using two Affymetrix
miRNA arrays: miRNA-1_0 and miRNA-1_0_2xgain.  The data are supposed
to be analyzed together but the problem is that the expression profiles
from both arrays look very different.  Here's what I did so far:
 - Normalized both datasets separately using APT.
   I used APT because to my knowledge there is no CDF package for the
   2xgain array in Bioconductor.
 - Then I applied an additional quantile normalization step using limma.
The problem is that even with that, the datasets have very different
profile patterns (when I do a PCA plot, 96% of the variance is explained
by the difference in array types).

I was hoping that maybe someone here has encountered this type of a
problem before, and would be willing to share his/her thoughts.

Best regards,

Michal Blazejczyk
FlexArray Lead Developer
McGill University and Genome Quebec Innovation Centre
http://genomequebec.mcgill.ca/FlexArray