[BioC] question with reading bead summary data into beadarray

[Mark Dunning]

Hi,

It looks like there is a typo in your command. The qc.columns argument
should be;

qc.columns=list(exprs="AVG_Signal",Detection="Detection Pval")

and you had mis-typed Dectection as Dectection. Sorry the error
message wasn't more informative in diagnosing the problem. The names
of the qc columns have to match the names in the ExpressionSet object
so that the control probes can get appended correctly to the main
expression matrix.

Regards,

Mark


On Tue, May 1, 2012 at 5:36 PM, Ou, Jianhong <Jianhong.Ou at umassmed.edu> wrote:
> 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 at umassmed.edu<mailto:jianhong.ou at umassmed.edu>
>
>
>
>        [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor