hi i try to make an analysis of a micro array from nimblegen (oligonucleotides one channel) for example to do a boxplot i follow the instruction in the pdf "02 - NimbleGen Expression and Preprocessing" but i don't know how to make this, with one channel, how can i do ? here my code : > xys.files <-list.xysfiles(full.names = TRUE) > xys.files [1] "./88693_532.xys" "./89430_532.xys" "./96225_532.xys" "./96252_532.xys" > basename(xys.files) [1] "88693_532.xys" "89430_532.xys" "96225_532.xys" "96252_532.xys" > theData <-data.frame(Key = rep(c("cals", "embryon"), each = 2)) > is.data.frame(theData) [1] TRUE > rownames(theData) <- basename(xys.files) > vm <- data.frame(chanel = factor("_ALL_", levels = c("channel1", "channel2", "_ALL_")), labelDescription = "oryza sativa") > pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vm) > test <-read.xysfiles(xys.files, phenoData = pd) when i do this i got the error : > test <-read.xysfiles(xys.files, phenoData = pd) Platform design info loaded. Checking designs for each XYS file... Done. Allocating memory... Done. Reading ./88693_532.xys. Reading ./89430_532.xys. Reading ./96225_532.xys. Reading ./96252_532.xys. Erreur dans validObject(out) : invalid class "ExpressionFeatureSet" object: 'NChannelSet' varMetadata must have a 'channel' column here my session info () : R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8 [5] LC_MONETARY=C LC_MESSAGES=fr_FR.utf8 [7] LC_PAPER=fr_FR.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.2006.07.24.picaud.dbretro_0.0.1 RSQLite_0.9-2 [3] DBI_0.2-5 RColorBrewer_1.0-2 [5] limma_3.4.5 genefilter_1.30.0 [7] maqcExpression4plex_1.2 oligo_1.12.2 [9] oligoClasses_1.10.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affxparser_1.20.0 affyio_1.16.0 annotate_1.26.1 [4] AnnotationDbi_1.10.2 Biostrings_2.16.9 IRanges_1.6.17 [7] preprocessCore_1.10.0 splines_2.11.1 survival_2.35-8 [10] tools_2.11.1 xtable_1.5-6 and my traceback () > traceback() 3: stop(msg, " ", errors, domain = NA) 2: validObject(out) 1: read.xysfiles(xys.files, phenoData = pd) -- MOZAR Michaël Master Bioinformatique Université de Nantes 0688715937 [[alternative HTML version deleted]]