Dear list, when I try to read the Illumina beadarray control probe profile using readBeadSummaryData library(beadarray) dataFile = "Spag4_data.txt" qcFile = "Spag4_con.txt" BSData = readBeadSummaryData(dataFile = dataFile, dec=",", qcFile = qcFile, skip = 0, qc.skip = 0) I get Error in if (!is.na(typeCol)) { : argument is of length zero Does anyone know what this could mean? The error must be related to the qcFile, when I skip reading it everything works as expected... Many thanks, Moritz (Fellow, University of Bonn, Germany) My sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.0.2 Biobase_2.10.0 loaded via a namespace (and not attached): [1] limma_3.6.9 tools_2.12.0 [[alternative HTML version deleted]]

Hi Moritz, Looking at the code, it seems that beadarray is expecting a column called TargetID in the QC file. I think this indicates what type of control (e.g. negative, housekeeping each line represents). Do you have such a column in your file? I'm afraid the code in beadarray isn't robust to the situation where this column doesn't exist. Regards, Mark On Thu, Jan 13, 2011 at 4:10 PM, Moritz Kebschull <endothel at="" gmail.com=""> wrote: > Dear list, > > when I try to read the Illumina beadarray control probe profile using > readBeadSummaryData > > library(beadarray) > dataFile = "Spag4_data.txt" > qcFile = "Spag4_con.txt" > BSData = readBeadSummaryData(dataFile = dataFile, dec=",", qcFile = qcFile, > skip = 0, qc.skip = 0) > > I get > > Error in if (!is.na(typeCol)) { : argument is of length zero > > Does anyone know what this could mean? > The error must be related to the qcFile, when I skip reading it everything > works as expected... > > Many thanks, > > Moritz (Fellow, University of Bonn, Germany) > > > My sessionInfo() > > R version 2.12.0 (2010-10-15) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=German_Germany.1252 ?LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] beadarray_2.0.2 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] limma_3.6.9 ?tools_2.12.0 > > ? ? ? ?[[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 >