Hi~I have known that the genotyping of the ROS and MAP subjects was performed on the Affymetrix Genome-Wide HumanSNP Array6.0 (n = 1,709) and the Illumina OmniQuad Express platform (n = 384). Therefore, when I download the genotype data online (URL: https://www.synapse.org/#!Synapse:syn3157325), I found that there are two parts of genotype data??ROSMAP genotype data chop_Illumina and ROSMAP arrayGenotype data (Is the equivalent of Affy.6.0?). Could you please tell me which genotype data (Illumina or Affy.6.0) should be selected for analysis? or both for analysis?

Created by xiaoyan li adelalady
The CHOP data appear to be in hg19, but the Affy genotyped samples appear not to be. I suspect they're in hg18. The QC steps are described in the wiki on the Genotype Data folder.
Dear Solveig, Sorry to bother you again. I have download the genotype data online (syn3157325), incuding two batches of genotype data??ROSMAP genotype data chop_Illumina and ROSMAP arrayGenotype data. Could you please tell me whether these genotype data is both hg19 release?or not? If not, which is hg19? which is hg18? Another question is whether these uploaded genotype data are both already quality-controlled? Thanks so much and have a nice day. Best, XiaoYan
@adelalady - The two genotyping sets contain different individuals, so depending on which subjects you're interested in, you may want one, the other or both. If you want all subjects, I suggest using both. Solly

consulting ROSMAP genotype data? which one I should selected? page is loading…