The snpaffycomp project will provide a benchmark for genotyping algorithms for Affymetrix SNP arrays. A description of the comparison will soon appear in Genome Biology:
Lin S, Carvalho B, Cutler D, Arking D, Chakravarti A, Irizarry RA (2008) Validation and Extension of an Empirical Bayes Method for SNP Calling on Affymetrix Microarrays.
To participate in the comparison you will need at least one of the following datasets
A webtool where you can upload results and receive a report is under construction. Meanwhile you can contact us email@example.com and we can try to run the analysis for you.