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Notes on using SNP Scanner software from Princeton

Software is available here: http://genomics-pubs.princeton.edu/SNPscanner/

August 2008

Affy CEL file types

SNPScanner depends on version 3 ascii CEL files. Modern Affy systems (2008) using Command Console produce version 4 CEL files. However, there are two types of version 4 CEL files. Affy provides two utilities for converting CEL files. The windows utility: cellfileconversiontool.exe will not convert version 4 files produced by Command Console to version 3, however the Affy Power Tools suite has a conversion utility that will interconvert all three file types.