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Dear Tim, My fault. I introduced an "improvement" to read.ilmn() on 31 January, but forgot that the Illumina probe IDs might not all be unique and so might not be allowable as rownames for the gene annotation data.frame. I have fixed it today. The limma change-log tells the story: 5 February 2014: limma 3.18.11 - The change to read.ilmn() in 3.18.10 caused an error when the Illumina probe IDs were not all unique. The probe IDs are now used as row.names for the annotation data.frame only when they are unique. 31 January 2014: limma 3.18.10 - read.ilmn() now sets the same probe IDs as rownames for both the expression matrix E and the annotation data.frame genes. Best wihes Gordon ------------- original message ------------- Tim Kendall Tim.Kendall at ed.ac.uk Tue Feb 4 16:50:13 CET 2014 Hi, I am trying to follow the case study ("16.3 Comparing Mammary Progenitor Cell Populations with Illumina BeadChips") using the example data files (from http://bioinf.wehi.edu.au/marray/IlluminaCaseStudy/) in the limma User's Guide prior to my first attempt at analysing my own data in the same BeadStudio profile format. The target file reads without a problem but the /read.ilmn/ command fails to generate the expected EListRaw object from the profiles; I had a brief fiddle with my own data last week and successfully created an EListRaw object but I think there was an update to limma 3.18.10 that I applied before I tried the case study (and I can no longer successfully read my own data after the upgrade either). "/> source("http://bioconductor.org/biocLite.R")// //Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help// //> library("limma")// //.....// //> x <- read.ilmn(files="probe profile.txt",ctrlfiles="control probe profile.txt", other.columns="Detection")// //Reading file probe profile.txt ... ...// //Reading file control probe profile.txt ... ...// //Error in `row.names<-.data.frame`(`*tmp*`, value = c(5090180L, 6510136L, : // // duplicate 'row.names' are not allowed// //In addition: Warning message:// //non-unique values when setting 'row.names': '1110170', '2510500', '4010327', '4610291'/ " For information, output of traceback attached and output from sessionInfo(): "/> sessionInfo()// //R version 3.0.2 (2013-09-25)// //Platform: x86_64-pc-linux-gnu (64-bit)// // //locale:// // [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 // // [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 // // [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C // //[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C // // //attached base packages:// //[1] stats graphics grDevices utils datasets methods base // // //other attached packages:// //[1] limma_3.18.10 BiocInstaller_1.12.0// // //loaded via a namespace (and not attached):// //[1] tools_3.0.2/" I haven't been able to find reports of anything similar with limma and I hope I'm missing something simple - apologies if that's the case. Cheers, Tim -------------- next part -------------- A non-text attachment was scrubbed... Name: traceback.pdf Type: application/pdf Size: 29715 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140204="" a4db="" fa1a="" attachment.pdf=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140204="" a4db="" fa1a="" attachment.pl=""> ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}