We're using Affymetrix HG-U133_Plus_2 arrays and our experiment was done so that 8 of our samples were run initially as a test run, followed by running the remaining 74 samples. Since these were two different runs, I'm pre-processing them differently i.e. running rma on them separately. Is there a way to combine the two datasets after their probe level intensities have been normalized within each run since I want to include the initial 8 samples for differential gene expression analysis? If not, what is the best way to include the 8?
Please let me know.
Thanks!

	[[alternative HTML version deleted]]

