[BioC] beadarray illumina Human610-Quadv1_B.bpm

[Nolwenn Le Meur]

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 Santé-Environnement-Travail

IRISA Symbiose D151
Université 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