Maybe you could use the expresso() function from the affy library and only do the summarization step (i.e. skip normalization background correction etc). Should give you what I *think* you're looking for. Paul. On Wed, May 18, 2011 at 11:22 AM, Saurabh Bundela <saurabh.bundela at="" gmail.com=""> wrote: > Hi, > > Well I am not very sure, how to get exactly get it.... However you can get > probe level intensity data (Perfect match and Mis-match probes) using affy > methods like probes, pm, mm etc. > > Please try this code > > data<-ReadAffy() > pm<-as.data.frame(probes(data,which="pm")) > mm<-as.data.frame(probes(data,which="mm")) > names(pm)[1]<-"ProbesetID" > names(mm)[1]<-"ProbesetID" > write.table(pm,"PM.txt",sep="\t") > write.table(mm,"MM.txt",sep="\t") > > This should give two files with probe intensities from perfect match and mis > match probes, hope it'll be useful > > Best Regards, > > Saurabh > > > On Wed, May 18, 2011 at 3:10 PM, Assa Yeroslaviz <frymor at="" gmail.com=""> wrote: > >> Hi, >> >> thanks for the response. Unfortunately this wasn't what I meant. >> I know about the way of extracting the normalized data. What I want is the >> raw data values for each of the probes on a probes set. >> >> Assa >> >> On Wed, May 18, 2011 at 10:31, Saurabh Bundela <saurabh.bundela at="" gmail.com="">wrote: >> >>> Hi, >>> >>> I think you can first convert AffyBatch obejct into ExpressionSet data >>> type (by using preprocessing algorithms like rma, plier, gcrma etc) and than >>> by using method 'exprs' you should get full matrix with probe names.... >>> >>> >>>sample code >>> >>> library(affy) >>> #Import cel files into R >>> data<-ReadAffy() >>> #preprocess AffyBatch object 'data' with RMA >>> data2<-rma(data) >>> #extracting matrix >>> data3<-exprs(data2) >>> #converting matrix to data frame >>> data4<-as.data.frame(data3) >>> names(data4)[1]<-"ProbesetID" >>> #exporting data matrix to external tab-delimited file for downstream >>> analysis >>> write.table(data4,"Data.txt",sep="\t") >>> <<<<<< >>> >>> >>> Best Regards, >>> >>> Saurabh >>> >>> On Wed, May 18, 2011 at 1:16 PM, Assa Yeroslaviz <frymor at="" gmail.com="">wrote: >>> >>>> Hi, >>>> >>>> I'm trying to extract a matrix of intensity values from an AffyBatch >>>> object. >>>> >>>> I know I can have them using >>>> > Intensity(AffyBatch) >>>> or >>>> >exprs(AffyBatch) >>>> >>>> but I would like to have a full matrix with the probe names. >>>> Unfortunately I can't find a way of doing it. >>>> >>>> There are several way of extracting the names of the probes, but not in >>>> the >>>> same order or magnitude compared to the intensity array. >>>> >>>> > length(geneNames(rawData))[1] 18952> length(probeNames(rawData))[1] >>>> 265358> dim(intensity(rawData))[1] 535824 ? ? 12> dim(exprs(rawData))[1] >>>> 535824 ? ? 12 >>>> >>>> Does anyone has an idea of how to extract these Values into a matrix. I >>>> have >>>> the original CEL files. >>>> >>>> Even a way outside of R will be welcome. >>>> >>>> Thanks >>>> >>>> Assa >>>> >>>> ? ? ? ?[[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 >>>> >>> >>> >> > > ? ? ? ?[[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 > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com