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" # 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'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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.16.4 -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland