Hi All, I used calcNormFactors function in edgeR to normalize my data : Normalized->calcNormFactors(data) However ,when i used it Normalized1->calcNormFactors(data,refColumn=1) I got slightly different normalization factors,The difference is about 0.02 between Normalized and Normalized1 for some libraries For me it was not expected as i thought the function considers the 1st column is the reference column by default.Any Comments?? Thank you and best regards Chris [[alternative HTML version deleted]]

Dear Chris Apr/23/12 2:50 PM, chris Jhon scripsit:: > Hi All, > > I used calcNormFactors function in edgeR to normalize my data : > > Normalized->calcNormFactors(data) > > However ,when i used it > > Normalized1->calcNormFactors(data,refColumn=1) > > > I got slightly different normalization factors,The difference is about 0.02 > between Normalized and Normalized1 for some libraries > For me it was not expected as i thought the function considers the 1st > column is the reference column by default.Any Comments?? It's always great to have thoughts, but sometimes it is more precise to check what it says in the documentation. For instance, the manual page of calcNormFactors says "If 'refColumn' is unspecified, the library whose upper quartile is closest to the mean upper quartile is used." Best wishes Wolfgang > Thank you and best regards > Chris > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber