I know that I can query the GEO database using the AnnBuilder package. However, I don't know exactly what to do next. NCBI states that the data they present in GDS accessions is normalized, but they don't explain how. The GSMs of different contributors not necessarily match, and they sometimes lack parts of the data. Also, if the raw data is submitted, how come they don't show the measurements for both repetitions of each gene in a cDNA array. Another problem, is that although the GDS are claimed to be normalized the sum of logs for all genes on a chip doesn't sum to 0. So, if anybody worked with GEO before, and has experience at it I would be glad to pose several more specific questions.