error with affycomp package
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Andrea Grilli ▴ 240
@andrea-grilli-4664
Last seen 6.5 years ago
Italy, Bologna, Rizzoli Orthopaedic Ins…
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
hgu133plus2 affycomp hgu133plus2 affycomp • 891 views
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@james-w-macdonald-5106
Last seen 9 days ago
United States
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
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