If we get the Microarray gene datasets with illumina platform, can we run normalisation through GEO2R?
Am I correct in assuming that the dataset is in GEO already? Otherwise, GEO2R would make no sense.
yes, dataset is already there in GEO.
Yes you can.
Here's a brief tutorial on how to run the data through GEO2R and upload your dataset to iPathwayGuide, in case that might be helpful.