Hi List,

Does anyone know of a package/tool/script that allows checking the integrity of (Affymetrix CEL) files?? [e.g. using comparisons of MD5 checksums]? 

I am asking because when transferring a data set via FTP unexpectedly a CEL file became corrupt. Upon uploading the files are automatically analyzed in our pipeline. It took us quite some time to find out that the problem was caused by one faulty file out of 16 (and not something else).

 
> data <- ReadAffy()
Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  : 
        Is D:/Guido/A42_7_Int_ko_wy.CEL really a CEL file? tried reading as text, gzipped text and binary
> 


This is the first time it happened to us, but now I realized that it would be very useful if after transferring the integrity of the CEL file could be checked, allowing the immediate identification of corrupt files.

Thanks,
Guido

------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands

internet:   http://nutrigene.4t.com
email:      guido.hooiveld@wur.nl


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