Hi, I tried to reproduce the example of the MAQC study described in V2NExpression.pdf. But, the command line maqc <- read.xysfiles(xys.files, phenoData = pd) gave the following output : Platform design info loaded. Checking designs for each XYS file... Done. Allocating memory... Done. Reading extdata/9868701_532.xys. Reading extdata/9868901_532.xys. Reading extdata/9869001_532.xys. Reading extdata/9870301_532.xys. Reading extdata/9870401_532.xys. Reading extdata/9870601_532.xys. Erreur dans validObject(out) : invalid class ???ExpressionFeatureSet??? object: NChannelSet levels(varMetadata(object)$channel) / assayDataElementNames() mismatch; see ?"channelNames<-,NChannelSet ,character-method" traceback() gave : > traceback() 3: stop(msg, ": ", errors, domain = NA) 2: validObject(out) 1: read.xysfiles(xys.files, phenoData = pd) Any suggestions would be appreciated, Thank you, Isabelle -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hg18.60mer.expr_3.4.0 RColorBrewer_1.0-5 limma_3.18.1 genefilter_1.44.0 maqcExpression4plex_1.6.3 pdInfoBuilder_1.26.0 oligo_1.26.0 [8] oligoClasses_1.24.0 affxparser_1.34.0 RSQLite_0.11.4 DBI_0.2-7 Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 annotate_1.40.0 AnnotationDbi_1.24.0 Biostrings_2.30.0 bit_1.1-10 codetools_0.2-8 ff_2.2-12 foreach_1.4.1 [9] GenomicRanges_1.14.3 IRanges_1.20.4 iterators_1.0.6 preprocessCore_1.24.0 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 [17] XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.