Dear all I'm having problems converting my Microarray data (Agilent.txt files) to soft files for subission to GEO using the packeage: GEOsubission I have 24 arrays (Agilent.txt files) in my experiment, the files "eRED.txt" and "dRED.txt" were setup according to the examples given in the vignette: > sampleID <- as.character(c(1:24)) > seriesName <- "blabla" > dataDir <- c("/ArrayDir") > microarray2soft(samplenames = sampleID, + sampleinfo = "dRED.txt", + seriesnames= seriesName, + seriesinfo = "ser.txt", + datadir = dataDir, + expressionmatrix = "eRED.txt") This alway returns the following ERROR messege: Error in microarray2soft(samplenames = sampleID, sampleinfo = "dRED.txt", : Column names in expression matrix do not match the names of raw microarray data files given in sampleinfo file. Which is puzzling, because when I read in the .txt files to R and check the column names for the expressionmatrix and the sample names in the sampleinfo file I do not find any problems: > sampDat <- read.delim(file.path(dataDir, "dRED.txt")) > expMatrix <- read.delim(file.path(dataDir, "eRED.txt")) > colnames(expDat) == sampDat$Sample_supplementary_file [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets grid methods [8] base other attached packages: [1] GEOsubmission_1.2.0 Biobase_2.10.0 limma_3.6.6 [4] reshape_0.8.3 plyr_1.2.1 proto_0.3-8 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 ggplot2_0.8.8 [4] preprocessCore_1.12.0 tools_2.12.0 If anyone happens to have any idea what could cause the error message please let me know best regards, Fabian [[alternative HTML version deleted]]