[BioC] 450K annotation: discrepancy between GEO GPL and Bioconductor annotation

[Bartlett, Thomas]

Hi,

I've noticed a discrepancy between the chromosome information given for some of the probes of the Illumina Infinium 450K array in the GEO GPL info, and in the corresponding Bioconductor annotation package.

The first four probes on the 450K GPL summary page on the GEO website 
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13534
in the 'data table' are cg00035864, cg00050873, cg00061679 and cg00063477, and the corresponding value in the CHR column is Y for all four of these. However, in the corresponding Bioconductor annotation package IlluminaHumanMethylation450k.db, using IlluminaHumanMethylation450kCHR the chromosome for these same 4 probes is given as Y, NONE, NONE and Y, respectively. N.B., the values in the MAPINFO column of 'data table' and those found using IlluminaHumanMethylation450kCPGCOORDINATE are identical for these 4 probes.

Is there any reason why there is this discrepancy, and might it be more widespread?

Thanks in advance for your help

Tom Bartlett