Dear list, I tried to compare raw summarized expression values coming from miRNA QC Tool (background detection, RMA global background correction, median polish summarization) to expresso output using line: expresso(afbatch=myabatch, bg.correct = TRUE, bgcorrect.method = "rma", normalize = FALSE, pmcorrect.method = "pmonly",summary.method = "medianpolish", verbose = TRUE,widget = FALSE) on the same set of CEL files, but they are quite different. Importing the same QC Tool cdf file "miRNA-1_0.cdf" in R library led to same results of standard bioconductor "mirna10cdf". I'm apparently using the same algorithms (RMA bg correction and median polish), but it seems there is something different between Affy QC tool processing and expresso procedure. Is this possible? Thanks all for any suggestion Giacomo Dr Giacomo Tuana Dipartimento di Scienze Mediche, Università degli Studi di Milano U.O. Ematologia 1 - CTMO Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico via Francesco Sforza, 35 20122 MILANO (Italy) tel. 0255033328 [[alternative HTML version deleted]]

Hi Giacomo, On 3/2/2011 12:23 PM, Giacomo Tuana wrote: > Dear list, > > I tried to compare raw summarized expression values coming from miRNA QC > Tool (background detection, RMA global background correction, median polish > summarization) to expresso output using line: > > expresso(afbatch=myabatch, bg.correct = TRUE, bgcorrect.method = "rma", > normalize = FALSE, pmcorrect.method = "pmonly",summary.method = > "medianpolish", verbose = TRUE,widget = FALSE) > > on the same set of CEL files, but they are quite different. Importing the > same QC Tool cdf file "miRNA-1_0.cdf" in R library led to same results of > standard bioconductor "mirna10cdf". I'm apparently using the same algorithms > (RMA bg correction and median polish), but it seems there is something > different between Affy QC tool processing and expresso procedure. Is this > possible? Of course. The algorithms have been implemented by two different groups, one of which isn't known for releasing complete details of their algorithms. So what you think you are doing with the miRNA QCTool may not in fact be what you are doing. In addition, I don't see an 'rma' style background correction for the miRNA QCTool in their user manual. It appears they are using a gcrma-type background correction. Best, Jim > > > Thanks all for any suggestion > > Giacomo > > > Dr Giacomo Tuana > Dipartimento di Scienze Mediche, Universit? degli Studi di Milano > U.O. Ematologia 1 - CTMO Fondazione IRCCS Ca' Granda Ospedale Maggiore > Policlinico > via Francesco Sforza, 35 > 20122 MILANO (Italy) > tel. 0255033328 > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues