First, I apologize if this is a stupid question. I am a grad-student and this is the first-time working with such data.
Per individual, I have 4,257,405 SNP probes from chromosomes 1-22. All these probes are recorded by their dbSNP RS IDs (e.g. rs13031737, rs62116682, etc). Some of the probes have questionable dbSNP RS IDs (chr2:132038:D, chr2:346071:I, etc) which relate to insertions and deletions but can't be searched for using the NHS database (https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?). I am assuming these dbSNP RS IDs may have been modified/edited but I am not exactly sure.
While I do have positions for all these probes, I am trying to obtain the latest build/annotation. I was told this is the "older" affy 6.0 chip and found the annotation file (http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_6). Problem is, when I download the latest build (e.g. GenomeWideSNP_6 Annotations, CSV format, Release 35 (313 MB, 4/30/15)), it appears to not contain the SNP IDs found in my data-files. Additionally, that csv file contains less than 1-million unique probes whereas my SNP data contains over 4-million.
Lastly, the SNP-position file....which I am trying to update with a more recent build... contains positions for many more SNPs (9,249,128 total) and includes the insertion/deletion nomenclature.
Thus, looking for feedback about what I may be doing wrong.