Hi It has been awhile since I used the lumi package and my old script does not work any more. I have tried to find out why but without luck. I am trying to load a GenomStudio file (SampleProbeProfile_non- normalized_GeneSpring.txt) using lumiR (dataSet <- lumiR(dataFil, sep = NULL, detectionTh = 0.5, na.rm = TRUE, convertNuID = FALSE, lib.mapping = illuminaHumanv3.db, dec = '.', parseColumnName=FALSE, checkDupId=TRUE, QC=TRUE, columnNameGrepPattern = list(exprs='AVG_SIGNAL', se.exprs='BEAD_STDEV', detection='Detection', beadNum='Avg_NBEADS'), inputAnnotation=FALSE, annotationColumn=c(),verbose=TRUE) ) And I get the following error message: Perform Quality Control assessment of the LumiBatch object ... Warning message: In lumiR(dataFil, sep = NULL, detectionTh = 0.5, na.rm = TRUE, convertNuID = FALSE, : The data file may not be in the Illumia BeadStudio or GenomeStudio output format. My sessionInfo: sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=Norwegian (Bokmål)_Norway.1252 LC_CTYPE=Norwegian (Bokmål)_Norway.1252 LC_MONETARY=Norwegian (Bokmål)_Norway.1252 [4] LC_NUMERIC=C LC_TIME=Norwegian (Bokmål)_Norway.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaHumanv3BeadID.db_1.6.0 org.Hs.eg.db_2.4.1 GOstats_2.14.0 graph_1.26.0 [5] Category_2.14.0 statmod_1.4.6 lumi_1.14.0 MASS_7.3-6 [9] preprocessCore_1.10.0 mgcv_1.6-2 affy_1.26.1 annaffy_1.20.0 [13] KEGG.db_2.4.1 GO.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 [17] annotate_1.26.1 AnnotationDbi_1.10.2 Biobase_2.8.0 xtable_1.5-6 [21] RColorBrewer_1.0-2 limma_3.4.4 loaded via a namespace (and not attached): [1] affyio_1.16.0 genefilter_1.30.0 grid_2.11.1 GSEABase_1.10.0 lattice_0.18-8 Matrix_0.999375-39 nlme_3.1-96 [8] RBGL_1.24.0 splines_2.11.1 survival_2.35-8 tools_2.11.1 XML_3.1-1 > My traceback: > traceback() No traceback available Any idea why? Regards, Ingrid [[alternative HTML version deleted]]