Dear mailing list, I'm trying to use affycomp package, but I'm confused on how to move to my CEL data files. I read the package documentation, did google search, and I also went into the "read.dilution/read.spikein" functions, understanding that there is some problem with the phenodata, but I cannot carry on to the next steps. Any suggestions? Also one doubt, could the package be used also on HGU133 plus 2 platform? Thanks, Andrea This is my script: library("affy") library("hgu133plus2.db") Data = ReadAffy() # import .CEL files eset.rma <- rma(Data) write.table(data.frame(exprs(eset.rma), check.names=FALSE), file="eset.rma.csv", sep=",", col.names=NA, quote=FALSE) # save expression file library("affycomp") d <- read.spikein("eset.rma.csv", cdfName=c("hgu133a"), remove.xhyb=TRUE) Error in `[.data.frame`(s, , sampleNames(pd)) : undefined columns selected s <- read.newspikein("eset.rma.csv") Error in `[.data.frame`(s, , sampleNames(pd)) : undefined columns selected > sessionInfo() R version 2.14.2 (2012-02-29) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools tcltk stats graphics grDevices utils datasets [8] methods base other attached packages: [1] hgu133plus2cdf_2.9.1 tkWidgets_1.32.0 DynDoc_1.32.0 [4] widgetTools_1.32.0 hgu133plus2.db_2.6.3 org.Hs.eg.db_2.6.4 [7] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.19 [10] gcrma_2.26.0 affycomp_1.30.2 affy_1.32.1 [13] Biobase_2.14.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 BiocInstaller_1.2.1 Biostrings_2.22.0 [4] IRanges_1.12.6 preprocessCore_1.16.0 splines_2.14.2 [7] zlibbioc_1.0.1 Dr. Andrea Grilli andrea.grilli at ior.it phone 051/63.66.756 Laboratory of Experimental Oncology, Development of Biomolecular Therapies unit, Rizzoli Orthopaedic Institute Codivilla Putti Research Center via di Barbiano 1/10 40136 - Bologna - Italy

Hi Andrea, On 4/20/2012 6:49 AM, andrea.grilli at ior.it wrote: > Dear mailing list, > I'm trying to use affycomp package, but I'm confused on how to move to > my CEL data files. I read the package documentation, did google > search, and I also went into the "read.dilution/read.spikein" > functions, understanding that there is some problem with the > phenodata, but I cannot carry on to the next steps. Any suggestions? I think you misunderstand the purpose of the affycomp package. This package isn't designed to work with your data, it is designed to work with the Affy and GeneLogic spike-in datasets. The goal of the package is to make it easy for people to compare their preferred summarization methods easily. Best, Jim > Also one doubt, could the package be used also on HGU133 plus 2 platform? > Thanks, > Andrea > > > This is my script: > library("affy") > library("hgu133plus2.db") > > Data = ReadAffy() # import .CEL files > eset.rma <- rma(Data) > write.table(data.frame(exprs(eset.rma), check.names=FALSE), > file="eset.rma.csv", sep=",", col.names=NA, quote=FALSE) # save > expression file > > library("affycomp") > d <- read.spikein("eset.rma.csv", cdfName=c("hgu133a"), remove.xhyb=TRUE) > > Error in `[.data.frame`(s, , sampleNames(pd)) : > undefined columns selected > > s <- read.newspikein("eset.rma.csv") > > Error in `[.data.frame`(s, , sampleNames(pd)) : > undefined columns selected > > > >> sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools tcltk stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] hgu133plus2cdf_2.9.1 tkWidgets_1.32.0 DynDoc_1.32.0 > [4] widgetTools_1.32.0 hgu133plus2.db_2.6.3 org.Hs.eg.db_2.6.4 > [7] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.19 > [10] gcrma_2.26.0 affycomp_1.30.2 affy_1.32.1 > [13] Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 BiocInstaller_1.2.1 Biostrings_2.22.0 > [4] IRanges_1.12.6 preprocessCore_1.16.0 splines_2.14.2 > [7] zlibbioc_1.0.1 > > > > > Dr. Andrea Grilli > andrea.grilli at ior.it > phone 051/63.66.756 > > Laboratory of Experimental Oncology, > Development of Biomolecular Therapies unit, > Rizzoli Orthopaedic Institute > Codivilla Putti Research Center > via di Barbiano 1/10 > 40136 - Bologna - Italy > > _______________________________________________ > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099