Notes on using SNP Scanner software from Princeton

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

August 2008

• WARNING: SNPScanner depends on version 3 CEL files (see below), but will not report an error if started with other file versions. Instead it will appear to run INDEFINITELY.

• The README bug report address (ruderfer@princeton.edu) is out of date.

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.