[BioC] Combining Affymetrix miRNA samples from different arrays
michal.blazejczyk at mail.mcgill.ca
Thu Dec 9 18:41:40 CET 2010
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.
FlexArray Lead Developer
McGill University and Genome Quebec Innovation Centre
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