This dataset is expected to be useful for the development and evaluation of low-level analysis methods for making genotype calls from probe intensity data. It consists of 30 trios each analyzed on both the Xba and Hind array (so a total of 30x3x2=180 hybridizations). The trios are CEPH trios also used in the International HapMap Project .

Of particular use is the fact that the HapMap Project has made available a large number of reference genotypes which can be used in conjunction with this dataset. The HapMap data access policy limits redistribution rights on these genotypes so they cannot be made available directly by Affymetrix, but the reference data can be downloaded directly from the HapMap Project. As of HapMap release 16c1, a total of 30,000 SNPs have reference genotypes available for the samples shared here. These numbers are steadily increasing with each HapMap update.

The details of the analysis method used by GDAS to determine genotype calls based on probe intensity data have been published in Bioinformatics.

The dataset has been split into 11 parts for convenient download. These can be unzipped on top of one another. The file with the word ?base? in the filename is required, the other 10 zip files each contain distinct collections of chip data and users wanting to download only a subset of the data may pick a subset of these zips.

The data is provided in two versions. Each version contains the same data but in different file formats. Version 1 (in table 1) contains raw CEL, CHP and EXP files and is suitable for use outside of the GCOS/GTYPE framework. It is expected to be mainly of interest for users interested in low-level probe analysis. Version 2 (in table 2) contains DTT format files for integration with the GCOS/GTYPE framework and is expected to be mainly of interest for users wishing to integrate the data with these applications.

In either case there is a file named README.txt provided in the 'base' file with detailed instructions on how to use the data. Md5 checksums are provided in the tables below for verification of the integrity of downloaded data.