I did some analysis using three different microarray platforms: Illumina v3, U133A and Agilent 4x44K. Each analysis was done separately and then overlapped the gene list by looking for genes in common.
I found 4 genes in common, however ....
How to choose the probe that best represents my genes (Probe) in common among the different platforms?
Choose the highest probe for each of the platforms? or do an average between probes?