I have two sets of data - one done on Affymetrix U133 and another on U133
Plus 2.0. The data sets are small - 3 control, 3 vector only and 3 vector +
construct for each (so, nine samples total).

Am I better off normalizing and analyzing differential expression within
each chip separately or is there some way to combine the data? I know I
can't do this simply because of the 6,000 extra probes on the Plus array,
but I wanted to see if anyone else had tackled a similar problem.

Thanks.

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