Hello :) I want to map GWAS SNPs (from http://www.genome.gov/gwastudies) to SNP IDs using R package (with pd.genomewidesnp.6). >From R package with this function (dbGetQuery), I could get all SNPs IDs information (906600 SNPs). But I found something strange. Because hundreds SNPs from GWAS couldn't map to SNP IDs (6.0 A???ymetrix arrays IDs, e.g., SNP_A-8682034). For example, I couldn't find these SNPs with R package: rs7023329 or rs7412746. Somebody can help me? Many thanks :) -- output of sessionInfo(): library(pd.genomewidesnp.6); con <- db(pd.genomewidesnp.6); ids_All <- dbGetQuery(con, "select man_fsetid from featureSet limit 906600;"); Info_All_add <- dbGetQuery(con, paste("select man_fsetid, dbsnp_rs_id, chrom, physical_pos, cytoband, allele_a, allele_b, gene_assoc from featureSet where man_fsetid in ('", paste(ids_All[,1], collapse="','"), "');", sep = "")); -- Sent via the guest posting facility at bioconductor.org.