Dear Group, I am integrating different microarray datasets from various affymetrix, cDNA (single and double channel) and illumuna arrays. I have couple of questions regarding this analysis. 1. Do I have to treat two channel arrays as two independent experiments/treatments to make it to the same page as one color or affymetrix data? 2. What kind of normalizations (between and with arrays) I need to keep in mind? I was normalizing within and between arrays in an individual experiment and finally scale the data to zero mean and unit standard deviation. Is this a reasonable approach? Or do I need to do one more normalization between all arrays (like quantile)? Greatly appreciate the feedback. Prasad