Hi This is more of a theory/litterature question than use of BioC. I know there are many different methods for quality control and preprocessing of affymetrix data, some use the mismatch probes, others don't. Does anybody know about reviews or comparative studies that compare the different methods and how they perform on data. A quick view of the bioconductor packages indicate that there are at least 5 packages that can be used for preprocessing of affymetrix data, how much do they differ? Best regards Ingunn Berget

Have a look at PMID: 15693945 It's a comparative analysis of many existing method using a defined dataset as a test bed. Emmanuel On 8/9/05, Ingunn Berget <ingunn.berget at="" umb.no=""> wrote: > Hi > This is more of a theory/litterature question than use of BioC. > > I know there are many different methods for quality control and > preprocessing of affymetrix data, some use the mismatch probes, others > don't. Does anybody know about reviews or comparative studies that compare > the different methods and how they perform on data. A quick view of the > bioconductor packages indicate that there are at least 5 packages that can > be used for preprocessing of affymetrix data, how much do they differ? > > > Best regards > Ingunn Berget > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi, you could also have a look at http://affycomp.biostat.jhsph.edu/ This provides a web-service comparing many different preprocessing methods, using 14 different criteria. You can sort the methods according to their performance in your "pet criterion". The according paper is linked there as well. Regards, Winnie Wefelmeyer Am 09.08.2005 um 13:42 schrieb Ingunn Berget: > Hi > This is more of a theory/litterature question than use of BioC. > > I know there are many different methods for quality control and > preprocessing of affymetrix data, some use the mismatch probes, others > don't. Does anybody know about reviews or comparative studies that > compare > the different methods and how they perform on data. A quick view of the > bioconductor packages indicate that there are at least 5 packages that > can > be used for preprocessing of affymetrix data, how much do they differ? > > > Best regards > Ingunn Berget > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >