Dear list Using the qpcrNorm package I can read single data files into R with readQpcr() but when I try to read in multiple files with readQpcrBatch() I'm getting an error and I don't understand what it's trying to tell me. Please see below. Many thanks John [john@y90-w-d RAT]$ R --vanilla R version 2.13.0 (2011-04-13) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-redhat-linux-gnu (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(qpcrNorm) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: limma Loading required package: affy > x<-readQpcr("RAT_CT2.csv") > slotNames(x) [1] "geneNames" "plateIndex" "exprs" "normalized" "normGenes" > rm(x) > x<-readQpcrBatch() Error in initialize(value, ...) : no slot of name "primerNames" for this object of class "qpcrBatch" > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] qpcrNorm_1.8.0 affy_1.28.1 limma_3.6.9 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 preprocessCore_1.12.0 > traceback() 4: initialize(value, ...) 3: initialize(value, ...) 2: new("qpcrBatch", geneNames = x@primerNames, plateIndex = x@plateIndex, exprs = x.data, normalized = FALSE, normGenes = x@normGenes) 1: readQpcrBatch() [[alternative HTML version deleted]]

John, It looks like one of the files in your directory is not properly formatted. See ?readQpcr (readQpcrBatch just calls readQpcr for each file). The function is expecting the first column to be gene/primer pairs, the second to be plate indices of each pari and the remaining columns are Ct values. The primerNames error you are seeing below pertains to the first column. To find the offending file you could try a loop with readQpcr on each file. Valerie On 06/01/11 03:57, John Coulthard wrote: > Dear list > > Using the qpcrNorm package I can read single data files into R with readQpcr() but when I try to read in multiple files with readQpcrBatch() I'm getting an error and I don't understand what it's trying to tell me. Please see below. > > Many thanks > John > > > [john at y90-w-d RAT]$ R --vanilla > > R version 2.13.0 (2011-04-13) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: i386-redhat-linux-gnu (32-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > >> library(qpcrNorm) >> > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: limma > Loading required package: affy > >> x<-readQpcr("RAT_CT2.csv") >> slotNames(x) >> > [1] "geneNames" "plateIndex" "exprs" "normalized" "normGenes" > >> rm(x) >> > > > >> x<-readQpcrBatch() >> > Error in initialize(value, ...) : > no slot of name "primerNames" for this object of class "qpcrBatch" > > > > >> sessionInfo() >> > R version 2.13.0 (2011-04-13) > Platform: i386-redhat-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C > [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 > [7] LC_PAPER=en_GB.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] qpcrNorm_1.8.0 affy_1.28.1 limma_3.6.9 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 preprocessCore_1.12.0 > >> traceback() >> > 4: initialize(value, ...) > 3: initialize(value, ...) > 2: new("qpcrBatch", geneNames = x at primerNames, plateIndex = x at plateIndex, > exprs = x.data, normalized = FALSE, normGenes = x at normGenes) > 1: readQpcrBatch() > > > [[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 >