Paul Geeleher <paulgeeleher at="" gmail.com=""> writes: > Hey Everyone, > > I'm having a problem reading some single channel GenePix data. > > I use the following code to read the files: > > # define column names > Cy3 <- "F543 Median" > Cy3b <- "B543 Mean" I don't think these are column headers in works.gpr... > # read targets and load data, the current directory contains the .gpr files > library("limma") > targets <- dir() > RG <- read.maimages( targets, > source='genepix',columns=list(R=Cy3,G=Cy3, Rb=Cy3b, Gb=Cy3b)) > > > Now I'm using exactly the same code for two different single channel > GenePix datasets, one works fine, the other throws this error after > trying to read the images (the last line above): > > """ > Error in read.table(file = file, header = TRUE, col.names = allcnames, : > duplicate 'row.names' are not allowed > """ I think the problem here is that a friendly piece of software has added tabs after the last field of each data record (and changed the encoding of file column names -- look after some of the Rgn R columns). I think you can get away with adding row.names=NULL to read.maimages but I'd check carefully that you've pulled in the right columns. Martin > I'm not sure what its referring to as both files have duplicate gene > names (which I presume are row names?). I've uploaded some samples of > files from either dataset: > > http://frink.nuigalway.ie/~pat/works.gpr > http://frink.nuigalway.ie/~pat/doesntWork.gpr > > > One more difference is that the files that don't work have a separate > GAL file. I don't know if this makes a difference. > > Thanks for any help folks. > > > > >> sessionInfo() > R version 2.8.1 (2008-12-22) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_ IE.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_IE.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] limma_2.16.4 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793