Affymetrix_Error_Rate is a simple program that identifies the error rate in files of Affymetrix microarray SNP data

Each Affymetrix microarray SNP 6.0 chip contains 2917 SNP probesets that are duplicated. Since each duplicate is analysed independantly of the other, by comparing the genotypes from each probeset in a pair it is possible to calculate the genotyping rate rate for each sample. When this data is combined with the number of 'Nocalls' in each file is possible to identify low quality data that should be either re-analysed or discarded.

The Affymetrix_Error_Rate program reads each of the *.birdseed-v2.txt text files in a folder and notes the total number of SNPs in the file, the number of SNPs with 'Nocall' gentoypes, the number of duplicate probsets and the number of duplicated probesets that have different genotypes for each probeset. This data is then saved to tab delimited text file called 'Errorrate.xls'. For Affymetrix_Error_Rate to correctly analysis each genotype file the chromosome and chromosomal position for each SNP must also be present in the *.birdseed-v2.txt files. This can be done by selecting the Include chromosomal position option in the Tab Delimited Export Options window of the Affymetrix Genotyping Console when exporting the SNP data.

Download here (This program was first published on the 4-Oct-2011).

Note: this program requires the .NET framework version 2.0 to be installed (available through Windows Update).