[BioC] beadarray illumina Human610-Quadv1_B.bpm

[Matthew Ritchie]

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


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