Hi All,

I have got ~400 CEL files that need to be normalized together. Affy batch can handle upto ~200 CEL files, if you have 400 you will get an error message right the beginning before even be worry about your memory capacity. Recently AffyPara has introduced that enables you to run a large batch on clusters. However, if I continue to normalized them in two 200 batches on a single machine. How different the results would be compare to normalizing all 400 together. These CEL files are from a RIL population the should pretty much homogeneous. 

Thanks,

Hamid
	[[alternative HTML version deleted]]

