[BioC] some mismatches between affymetrix CGOS MAS5 detection calls and BioC mas5calls

Morten Mattingsdal mortenm at inbox.com
Mon Dec 11 15:26:00 CET 2006

hello haiyan,
The "M" is a marginal call, and is a borderline "P" or "A". I think its 
common to consider a "marginal call" a "present call".

haiyan wu wrote:
> 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
> 	[[alternative HTML version deleted]]
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