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"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Vladimir, > > Vladimir Morozov wrote: >> Hi, >> >> mas5calls.AffyBatch is supposed to calulate prence p-vales: >> "The 'mas5calls' method for 'AffyBatch' returns an 'exprSet' with >> calls in the 'exprs' slot and p-values in the 'se.exprs'. The >> code{mas5calls} for 'ProbeSet' returns a list with vectors of >> calls and pvalues." >> >> Here is what I get from mas5call >> >>>dim(exprs(ab.mas5calls)) >> >> [1] 45101 157 >> >>>exprs(ab.mas5calls)[1:2,1:3] >> >> 139102 139103 139104 >> 1415670_at "P" "P" "P" >> 1415671_at "P" "P" "P" >> >> it is Ok >> >> >>>dim(se.exprs(ab.mas5calls)) >> >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "se.exprs", for >> signature "ExpressionSet" > > Yeah, it looks like there isn't an accessor function for this slot for > ExpressionSets. However, you can get the data directly: > > get("se.exprs", ab.mas5calls at assayData) Use > assayData(ab.mas5calls)[["se.exprs"]] instead. This uses the 'assayData' accessor to retrieve the assay data, and the '[[' subsetting function to select the 'se.exprs' element. Using the accessor provides some protection should the slot name change. Using '[[' provides some protection against assayData returning a 'list', which it is allowed to do. Martin > > Best, > > Jim > > > >> >> >> Any suggestions how presence p-values can be accessed >> >> Thnaks >> Vladimir >> >> [[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 > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Yes, sorry, the documentation is not adequate. I added assayData to ExpressionSet (pointing toward eSet, where the method is actually defined), and a little information to the eSet and AssayData documentation to indicate one way of getting the elements. While on the eSet page I was reminded of assayDataElement and assayDataElementNames, which provides a different ways of finding out about and manipulating the contents of assayData. Martin "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Martin, > > Martin Morgan wrote: >> Use >> >>>assayData(ab.mas5calls)[["se.exprs"]] >> instead. This uses the 'assayData' accessor to retrieve the assay >> data, and the '[[' subsetting function to select the 'se.exprs' >> element. Using the accessor provides some protection should the slot >> name change. Using '[[' provides some protection against assayData >> returning a 'list', which it is allowed to do. > > Is this in lieu of an se.exprs() accessor? If so it might be > worthwhile to add something to the ExpressionSet-class help page. I > don't see anything there for the assayData() accessor itself, nor > anything about how one might subset the output from this accessor > safely. > > Best, > > Jim > > >> Martin > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Hi Vladimir, Vladimir Morozov wrote: > Hi, > > mas5calls.AffyBatch is supposed to calulate prence p-vales: > "The 'mas5calls' method for 'AffyBatch' returns an 'exprSet' with > calls in the 'exprs' slot and p-values in the 'se.exprs'. The > code{mas5calls} for 'ProbeSet' returns a list with vectors of > calls and pvalues." > > Here is what I get from mas5call > >>dim(exprs(ab.mas5calls)) > > [1] 45101 157 > >>exprs(ab.mas5calls)[1:2,1:3] > > 139102 139103 139104 > 1415670_at "P" "P" "P" > 1415671_at "P" "P" "P" > > it is Ok > > >>dim(se.exprs(ab.mas5calls)) > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "se.exprs", for > signature "ExpressionSet" Yeah, it looks like there isn't an accessor function for this slot for ExpressionSets. However, you can get the data directly: get("se.exprs", ab.mas5calls at assayData) Best, Jim > > > Any suggestions how presence p-values can be accessed > > Thnaks > Vladimir > > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.