Hi Mark,

I am dealing with Illumina BeadArray data by beadarray package. I download the training data (AsuragenMAQC_BeadStudioOutput.zip) from http://www.switchtoi.com/datasets.ilmn and followed the your sample code:

> library("beadarray")
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique

Welcome to Bioconductor

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

Loading required package: ggplot2
Welcome to beadarray version 2.6.0
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
> setwd("~/Downloads/AsuragenMAQC_BeadStudioOutput")
> dataFile = "AsuragenMAQC-probe-raw.txt"
> qcFile = "AsuragenMAQC-controls.txt"
> BSData = readBeadSummaryData(dataFile,qcFile, controlID="ProbeID",skip=0,qc.skip=0,qc.columns=list(exprs="AVG_Signal",Dectection="Detection Pval"))
Error in QC[[index]] = data[[i]] :
  attempt to select less than one element
In addition: Warning message:
In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns,  :
  controlIDs non-unique: 6 repeated entries have been removed.

and
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/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_2.6.0    ggplot2_0.9.0      Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.18.0 BeadDataPackR_1.8.0  colorspace_1.1-1     DBI_0.2-5            dichromat_1.2-4      digest_0.5.2
 [7] grid_2.15.0          IRanges_1.14.2       limma_3.12.0         MASS_7.3-18          memoise_0.1          munsell_0.3
[13] plyr_1.7.1           proto_0.3-9.2        RColorBrewer_1.0-5   reshape2_1.2.1       RSQLite_0.11.1       scales_0.2.0
[19] stats4_2.15.0        stringr_0.6

Could you help me to figure out this problem? Thanks.

Yours sincerely,

Jianhong Ou

jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>



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