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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". morten 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > . > >

HaiYan, "mas5call" is an implementation, that is a physical realization of something that is described in a documentation. The effective presence of bugs in an implementation cannot be ruled out, but there are a number of other reasons for differences: numerical precision issues and rounding errors, but also a reader's interpretation of the described procedure. The best way to have MAS5.0 results as done by CGOS... is probably to use CGOS itself. However (and beside further statements on the nature of things), BioC is giving you the tools to investigate at the probe level why these 300 probesets are either M or P, and decide for yourself (and eventually send us a bug report if you find a mistake on our side). If the these genes pass from one side to the other, they could be close to the borderline in the first place. Hoping this helps, L. > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > !DSPAM:457d68ac276685618593157! > > >