I would like to preprocess the microarry dataset GSE9006 which is Gene expression in PBMCs for children with diabetes. The array platforms are two, Affymetrix Human Genome HG-U133A and Affymetrix Human Genome HG-U133B. I need to combine two platform to increase the number of samples (n) and then analyse them for geting differential expression for each genes is it enough to download the data and normalize the expression matrix for each platform then merge them according to Gene Entrez? Thanks a lot for your cooperation
Please take a look at some of the comments here: How to integrate multiple data sets from microarray platform prior meta-analysis?
The ideal situation would be to use just the common genes and then include 'ArrayVersion' as a covariate in all downstream statistical analyses. I'm not sure there is any ideal way to use genes that don't overlap - where they don't overlap, the values would just have to be NA in samples were there's no data.