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Hi Ingrid, You need to update the lumi package. This problem should have been solved. The current version of lumi is 1.0.10. Version 1.1.0 will be released next week, which will include several new features, including support of BeadStudio 3.0 format, adding a lumiB function to allow user adding background correction and a lumiExpresso function to encapsulate all the preprocessing functions. A QC slot will be added in the LumiBatch class and the LumiQC class will be removed. Thanks! Pan -------- Original Message -------- Subject: [BioC] Error in rowname in lumiR? Date: Thu, 22 Mar 2007 09:31:50 +0100 From: Ingrid H. G. ?stensen <ingrid.h.g.ostensen@rr-research.no> To: <bioconductor at="" stat.math.ethz.ch=""> Hi I posted a message yesterday regarding the lumi package. I have been looking at the code for the lumiR procedure and found the line were things are going wrong: rownames(allData) <- targetID The error message that comes is: Error in `row.names<-.data.frame`(`*tmp*`, value = c("ILMN_10000", "ILMN_100000", : duplicate 'row.names' are not allowed Is seems that rownames can not see the difference between the different Illumina target ID?s, example of ID: ILMN_10000 ILMN_100000 ILMN_100007 ILMN_100009 ILMN_10001 ILMN_100010 ILMN_10002 ILMN_100028 ILMN_100030 ILMN_100031 ILMN_100034 ILMN_100037 ILMN_10004 ILMN_10005 ILMN_100054 ILMN_100059 ILMN_10006 ILMN_100075 ILMN_100079 ILMN_100083 ILMN_100084 ILMN_100086 ILMN_10009 ILMN_100091 ILMN_100097 ILMN_1001 ILMN_10010 ILMN_100101 ILMN_100106 ILMN_10011 ILMN_100114 ILMN_10012 More information: class(allData) [1] "data.frame" class(targetID) [1] "character" sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokm?l)_Norway.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: xtable RColorBrewer limma lumi mgcv affy affyio Biobase "1.4-3" "0.2-3" "2.9.13" "1.0.3" "1.3-23" "1.12.2" "1.2.0" "1.12.2" Does anyone have any suggestions about what might be wrong, can it be because I use R 2.4.1 and the package is for R 2.5.x? Or can it be something with the data file that contains the Illumina data. Regards, Ingrid [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor