[BioC] beadarray illumina Human610-Quadv1_B.bpm
Matthew Ritchie
mritchie at wehi.EDU.AU
Sun Jul 25 06:47:06 CEST 2010
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}}
More information about the Bioconductor
mailing list