library(GEOquery) gpl <- getGEO('GPL8887', destdir='.') head(Table(gpl), n=2) ID Chr MapInfo SNP_ID 1 200003 9 139026180 200003 2 200006 9 139046223 200006
But what does this mean?
- Does the column SNP_ID correspond to the rs identifier in dbSNP? Apparently no, as rs200003 is not on chr9.
- Does the column MapInfo correspond to the SNP coordinate? If yes, on which version of the human genome reference sequence is it mapped? hg18 or hg19?
I search on the Internet (on Illumina's web site, etc) but couldn't find any information. Any idea?