Hello, I am trying to combine and analyze together 2 microarray datasets from the same platform (Agilent single channel) that were scanned with 2 different scanners (one with Agilent scanner and one with Genepix). The datasets have the same number of genes, but because they were generated on two different scanners the outputs are different. My ultimate goal is to determine differentially expressed genes from the combined datasets. I have been using limma and have thus far created two separate RGlist objects and normalized each dataset separately. But I'm wondering if it's best to normalize the datasets separately first and then use the merge function to combine them or if it's recommended to merge them and then normalize the datasets together.
Any suggestions are great appreciated. Thanks for your help in advance!