Hi, I am trying to remove probes called A (absent) in all my microarray samples. I am trying to get the p-values for the probes across all samples so I can use genefilter to create a mask and select the present genes. However, I get the following error: > data<-ReadAffy() > rawcalls<-mas5calls(data) Getting probe level data... Computing p-values Making P/M/A Calls > se.exprs(rawcalls) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "se.exprs", for signature "ExpressionSet" se.exprs is supposed to give me the p.values, isn't it? Help is much appreciated, thanks, -- Hernando Martínez Vergara [[alternative HTML version deleted]]

HI Hernando Is this any use: #get rid of absent probes dataIn <- ReadAffy() masData <- mas5(dataIn) calls <- mas5calls(dataIn) calls <- exprs(calls) absent <- rowSums(calls == 'A') absent <- which (absent == ncol(calls)) dataFiltered <- masData[-absent,] iain --- On Thu, 8/7/10, Hernando Mart?nez <hernybiotec at="" gmail.com=""> wrote: > From: Hernando Mart?nez <hernybiotec at="" gmail.com=""> > Subject: [BioC] removal of probes called "Absent" > To: Bioconductor at stat.math.ethz.ch > Date: Thursday, 8 July, 2010, 11:48 > Hi, I am trying to remove probes > called A (absent) in all my microarray > samples. > I am trying to get the p-values for the probes across all > samples so I can > use genefilter to create a mask and select the present > genes. However, I get > the following error: > > > data<-ReadAffy() > > rawcalls<-mas5calls(data) > Getting probe level data... > Computing p-values > Making P/M/A Calls > > se.exprs(rawcalls) > Error in function (classes, fdef, mtable)? : > ? unable to find an inherited method for function > "se.exprs", for signature > "ExpressionSet" > > se.exprs is supposed to give me the p.values, isn't it? > > Help is much appreciated, thanks, > > -- > Hernando Mart?nez Vergara > > ??? [[alternative HTML version deleted]] > > > -----Inline Attachment Follows----- > > _______________________________________________ > 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

Hi Hernando, try: pvals <- assayData(rawcalls)[["se.exprs"]] Cheers, Cei Hernando Mart?nez wrote: > Hi, I am trying to remove probes called A (absent) in all my microarray > samples. > I am trying to get the p-values for the probes across all samples so I can > use genefilter to create a mask and select the present genes. However, I get > the following error: > >> data<-ReadAffy() >> rawcalls<-mas5calls(data) > Getting probe level data... > Computing p-values > Making P/M/A Calls >> se.exprs(rawcalls) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "se.exprs", for signature > "ExpressionSet" > > se.exprs is supposed to give me the p.values, isn't it? > > Help is much appreciated, thanks, > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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