I'm working with an Axiom Human Origins Array. The samples have been typed in two separate plates and the PCA is clearly showing the separation between the two batches. I guess I'm facing a batch effect. I'd like to normalize the array data and start over with the work. So far, I've been trying with dChip but it says that the required CDF file I provided is "Not a CDF file or not in text format" (I downloaded it from the Affymetrix web page, and I can't see what's wrong with it). If you have any suggestion, it would be helpful, not only on dChip, but even on how to deal with the batch effect and how to perform a normalization of the data.
Hi F.R. I have the exact same problem. Can you please summarize quickly how you dealt with it?! I would appreciate a lot!!