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

  1. 269 Affy HapMap 100K high quality arrays (6.8Gb)
  2. 270 Affy HapMap 500K high quality arrays (14.6Gb)
  3. 270 Affy HapMap 6.0 high quality arrays (10Gb)
  4. 152 Affy HapMap 500K first pass arrays (4.7Gb)
  5. 95 Broad HapMap 500K first pass arrays (8.2Gb)
  6. 44 Chakravarti HapMap 6.0 first pass arrays (2.8Gb)
  7. 96 Chakravarti HapMap 6.0 first pass arrays (4.0Gb)
  8. 40 Chakravarti replicate Xba chips (496Gb)
  9. 16 Chakravarti replicate Nsp chips (373Mb)
  10. NIHM Autism Xba chips
  11. NIHM Nsp chips
Note: for datasets 10 and 11 you need permission from NIHM.

A webtool where you can upload results and receive a report is under construction. Meanwhile you can contact us rafa@jhu.edu and we can try to run the analysis for you.