Hi,all
Recently I download some CEL files from GEO and get it's detection
calls using BioC mas5calls . When I compare this file with standard file
produced by Affymetrix company's CGOS platform,I found there are about 300
probesets called "M" by mas5call function but called "P" in my standard
file. These mismatches may affect our analysis result if we use detection
calls as a filter condition or for special algorithm using calls
infomation.  For many of us ,one may download CEL files from GEO or
ArrayExpress but can not get raw files contain detection calls from those
website.So we use BioC's mas5call function.But there are differences between
two method! What should I do?

Regards

haiyan

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