Batch Conversion Of Affymetrix Snp Ids To Refsnp Ids

Question

[user1202664]

How can I convert Affymetrix SNP IDs of the form - SNPA-8646962 - to RefSNP IDs (e.g. rs138274114 for SNPA-8646962). I can do this one-by-one via the dbSNP website (http://www.ncbi.nlm.nih.gov/projects/SNP/). However, I wish to convert hundreds of Affymetrix SNP IDs.

Answer 1

[David Quigley]

1) Get the annotation file your your array from Affymetrix's web site. For example, for Affy 6.0 you would want http://www.affymetrix.com/analysis/downloads/na32/genotyping/GenomeWideSNP_6.na32.annot.csv.zip. The first column is the Affy SNP ID. The second column is the dbSNP RS ID.

2) Use your favorite scripting tool or R to convert between column one and two.

3) Profit!

[Jorge Amigo]

sure user1202664 didn't realize that Affy chips come with this information. easy pointing to Affy website.