dear all, I recently tried to reload some old data anlysis which encompasses Illumina data from beastudio 1.5.13. Notably a chunck of code that previously work now does not any more. in particular: > filenames <- "myData.txt" > > r <- lumiR(filenames) Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : undefined columns selected looking in the man it seems that the package was updated to the new Illumina Bead Studio output. looking in the ma I guessed to put inputAnnotation=FALSE. but still nothing. r <- lumiR(filenames, inputAnnotation=FALSE) Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : undefined columns selected Now, I dont have the new software. what can I do? > sessionInfo() R version 2.7.2 (2008-08-25) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumi_1.6.2 mgcv_1.4-1 affy_1.18.2 [4] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1

Hi Claudio, Thanks for reporting the problem. I am not sure why it reported error when retrieving a missing column in a data.frame, usually it should return NULL instead of reporting error. To avoid this, please set the parameter convertNuID as FALSE, e.g., r <- lumiR(filenames, convertNuID=FALSE) It should solve the problem. Tell me if the problem still exists. Pan On 9/5/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Date: Thu, 4 Sep 2008 12:04:29 +0200 > From: "claudio\.is\@libero\.it" <claudio.is at="" libero.it=""> > Subject: [BioC] Lumi and Beadstudio 1.5.13 > To: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <k6o1bh$de2008fc6621fdeff2634e135b59a423 at="" libero.it=""> > Content-Type: text/plain; charset=iso-8859-1 > > dear all, > > I recently tried to reload some old data anlysis which encompasses Illumina > data from beastudio 1.5.13. > > Notably a chunck of code that previously work now does not any more. > in particular: > >> filenames <- "myData.txt" >> >> r <- lumiR(filenames) > Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : > undefined columns selected > > > looking in the man it seems that the package was updated to the new Illumina > Bead Studio output. > > looking in the ma I guessed to put inputAnnotation=FALSE. but still nothing. > > r <- lumiR(filenames, inputAnnotation=FALSE) > Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : > undefined columns selected > > Now, I dont have the new software. what can I do? > > >> sessionInfo() > R version 2.7.2 (2008-08-25) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;L > C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C; LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] lumi_1.6.2 mgcv_1.4-1 affy_1.18.2 > [4] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 ------------------------------------------------------ Pan Du, PhD Research Assistant Professor Northwestern University Biomedical Informatics Center 750 N. Lake Shore Drive, 11-176 Chicago, IL 60611 Office (312) 503-2360; Fax: (312) 503-5388 dupan at northwestern.edu