[BioC] Normalize data across platforms

[Steve Taylor]

Hi,

I have two sets of affy data CEL files. One set is from Hugene 1.0 ST arrays and the other from U133plus2 Arrays. I need to compare one set with another.

First I plan to use RMA to normalise the data set for each platform. I then plan to get a common reference id across the arrays, probably using ENSEMBL gene ID.
With the subset that have probes in common, what would be the best way to normalise across the arrays? Would quantile normalization using aroma.light be suitable?

Thanks for any advice,

Steve
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Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University