Dear list,

I am trying to follow the new bead-summary tutorial

http://www.bioconductor.org/packages/release/bioc/vignettes/beadarray/inst/doc/beadsummary.pdf

However, I end up with a ‘subscript out of bounds’ error. Does anyone happen
to know what´s wrong?

> library(beadarray)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Welcome to beadarray version 2.0.1
There have been major changes to beadarray since Bioconductor 2.6 (April
2010). Please see package vignette for details
> dataFile = "AsuragenMAQC-probe-raw.txt"
> qcFile = "AsuragenMAQC-controls.txt"
> BSData = readBeadSummaryData(dataFile = dataFile, qcFile = qcFile,
controlID = "ProbeID", skip = 0, qc.skip = 0, qc.columns = list(exprs =
"AVG_Signal",Detection = "Detection Pval"))
Warning message:
In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns,
 :
  controlIDs non-unique: 6 repeated entries have been removed.

> BSData
ExpressionSetIllumina (storageMode: list)
Error in object@channelData[[1]] : subscript out of bounds
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] beadarray_2.0.1 Biobase_2.10.0

loaded via a namespace (and not attached):
[1] limma_3.6.6
>

Many thanks,

cheers, Moritz


Moritz Kebschull
Fellow
Clinical Research Unit 208
University of Bonn, Germany

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