Hi Matt, I finally had time to ask for and get the idat files. I immediately tried the readIdatFiles function from crlmm package but got the following error: library(crlmm) samples <- read.csv("../idat/sampleSheet.csv", as.is=TRUE) RG <- readIdatFiles(sampleSheet=samples, arrayNames=NULL, ids=NULL, path= "../idat", arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"), highDensity=TRUE, sep="_", fileExt=list(green="Grn.idat", red="Red.idat"), saveDate=FALSE) reading 4861481038_R01C01 _Grn.idat reading 4861481038_R01C02 _Grn.idat reading 4861481038_R02C01 _Grn.idat reading 4861481038_R02C02 _Grn.idat reading 4861481039_R01C01 _Grn.idat reading 4861481039_R01C02 _Grn.idat reading 4861481039_R02C01 _Grn.idat reading 4861481039_R02C02 _Grn.idat reading 4861481062_R01C01 _Grn.idat reading 4861481062_R01C02 _Grn.idat reading 4861481062_R02C01 _Grn.idat reading 4861481062_R02C02 _Grn.idat Error in storageMode(RG) = "lockedEnvironment" : object 'RG' not found Calls: readIdatFiles Execution halted sessionInfo() R version 2.12.0 Under development (unstable) (2010-04-09 r51652) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] crlmm_1.7.4 oligoClasses_1.11.1 Biobase_2.9.0 loaded via a namespace (and not attached): [1] affyio_1.17.3 annotate_1.27.0 AnnotationDbi_1.11.1 [4] Biostrings_2.17.8 bit_1.1-4 DBI_0.2-5 [7] ellipse_0.3-5 ff_2.1-2 genefilter_1.31.0 [10] IRanges_1.7.7 mvtnorm_0.9-9 preprocessCore_1.11.0 [13] RSQLite_0.9-1 splines_2.12.0 survival_2.35-8 [16] tools_2.12.0 xtable_1.5-6 Any idea why? Thank you Nolwenn Le Meur ----------------------- IRSET - Institut de Recherche en Sant?-Environnement-Travail IRISA Symbiose D151 Universit? de Rennes I Campus Beaulieu 35042 Rennes Cedex France Phone: +33 2 99 84 71 17 Fax: +33 2 99 84 71 71 E-mail: nlemeur at irisa.fr Web: http://www.irisa.fr/symbiose/nolwenn_le_meur

Hi Nolwenn, Thanks for pointing out this bug which was recently introduced! It should be fixed in version 1.7.6 which I've just checked in, so if you upgrade, you should be back in business. Apologies for the inconvenience. Best wishes, Matt > Hi Matt, > > I finally had time to ask for and get the idat files. I immediately > tried the readIdatFiles function from crlmm package but got the > following error: > > library(crlmm) > samples <- read.csv("../idat/sampleSheet.csv", as.is=TRUE) > RG <- readIdatFiles(sampleSheet=samples, arrayNames=NULL, > ids=NULL, path= "../idat", > arrayInfoColNames=list(barcode="SentrixBarcode_A", > position="SentrixPosition_A"), > highDensity=TRUE, sep="_", > fileExt=list(green="Grn.idat", red="Red.idat"), > saveDate=FALSE) > reading 4861481038_R01C01 _Grn.idat reading 4861481038_R01C02 > _Grn.idat reading 4861481038_R02C01 _Grn.idat reading > 4861481038_R02C02 _Grn.idat reading 4861481039_R01C01 _Grn.idat > reading 4861481039_R01C02 _Grn.idat reading 4861481039_R02C01 > _Grn.idat reading 4861481039_R02C02 _Grn.idat reading > 4861481062_R01C01 _Grn.idat reading 4861481062_R01C02 _Grn.idat > reading 4861481062_R02C01 _Grn.idat reading 4861481062_R02C02 > _Grn.idat Error in storageMode(RG) = "lockedEnvironment" : object > 'RG' not found > Calls: readIdatFiles > Execution halted > > sessionInfo() > R version 2.12.0 Under development (unstable) (2010-04-09 r51652) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] crlmm_1.7.4 oligoClasses_1.11.1 Biobase_2.9.0 > > loaded via a namespace (and not attached): > [1] affyio_1.17.3 annotate_1.27.0 AnnotationDbi_1.11.1 > [4] Biostrings_2.17.8 bit_1.1-4 DBI_0.2-5 > [7] ellipse_0.3-5 ff_2.1-2 genefilter_1.31.0 > [10] IRanges_1.7.7 mvtnorm_0.9-9 preprocessCore_1.11.0 > [13] RSQLite_0.9-1 splines_2.12.0 survival_2.35-8 > [16] tools_2.12.0 xtable_1.5-6 > > > Any idea why? > > Thank you > Nolwenn Le Meur ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}