[BioC] beadarray_1.7.6. problem/error with readBeadSummaryData()

Jenny Drnevich drnevich at uiuc.edu
Tue Mar 18 17:09:22 CET 2008

Hi Christian,

I've been working with Illumina data myself and also came across this 
error. The problem is that you're leaving the default value for 
ProbeID to "TargetID" (see ?readBeadSummaryData for a description of 
the arguments and their defaults), but you don't have a TargetID 
column in your dataFile. Although the vignette and help page for 
readBeadSummaryData both say the defaults are set for BeadStudio 
Version 3 output, I've found this not to be true, at least for the 
Mouse-6 array. In our case, there are a variety of different ID 
numbers that can be output from BeadStudio, including both a PROBE_ID 
and ProbeID (one's  unique and one's not necessarily unique, I forget 
which is which). You should look in your dataFile to see what is the 
name of the column that contains the IDs and indicate that in the 
call to readBeadSummaryData(). However, if the ID column contains 
non-unique IDs, they are completely thrown out (a WARNING message 
here would be nice!); you can check to see if the IDs came through by 
looking at the rownames of   exprs(BSData)[1:5,1:5]

Interestingly, none of the IDs I can output from BeadStudio match the 
probeIDs given in the IlluminaMouseV1 annotation package provided by 
BioC. I'm going to investigate this further and if I figure out 
what's going on, I'll send a message to the list.


At 10:34 AM 3/18/2008, Christian Kohler wrote:
>Dear Bioconductor-list,
>I recently started to go in for analysing Illumina (BeadChip) datasets
>with the help of the 'beadarray' package.
>As an Example R-script (within BeadSummaryExample) is provided, the
>introduction to this topic is quite straightforward.
>Until today, I used 'beadarray' in version 1.7.0 and the code snippets
>of the example script worked out fine.
>With 'beadarray' version 1.7.6. I experienced the following problem:
> >BSData <- readBeadSummaryData(dataFile, qcFile=qcFile,
>sampleSheet=sampleSheet,skip=7, columns=list(exprs="AVG_Signal",
>se.exprs="BEAD_STDEV", >NoBeads="Avg_NBEADS"),
>qc.columns=list(exprs="AVG.Signal", se.exprs="SeqVAR"),qc.sep=","
>,sep=",", qc.skip=7, annoPkg="illuminaHumanv1")
> >Error in `row.names<-.data.frame`(`*tmp*`, value = "ProbeID") :
> > invalid 'row.names' length
>Now, I am just wondering if other 'beadarray'-users came across this error .
> > sessionInfo()
>R version 2.6.2 (2008-02-08)
>attached base packages:
>[1] tools     stats     graphics  grDevices utils     datasets  methods
>[8] base
>other attached packages:
>  [1] beadarray_1.7.6      affy_1.16.0          preprocessCore_1.0.0
>  [4] affyio_1.6.0         geneplotter_1.16.0   lattice_0.17-4
>  [7] annotate_1.16.0      xtable_1.5-1         AnnotationDbi_1.0.4
>[10] RSQLite_0.6-3        DBI_0.2-3            Biobase_1.16.1
>[13] limma_2.12.0
>loaded via a namespace (and not attached):
>[1] KernSmooth_2.22-22 RColorBrewer_1.0-1 grid_2.6.2         rcompgen_0.1-17
>[5] tcltk_2.6.2
>Thanks a lot for any help/suggestions.
>Christian Kohler
>Institute of Functional Genomics
>Computational Diagnostics
>University of Regensburg (BioPark I)
>D-93147 Regensburg (Germany)
>Tel. +49 941 943 5055
>Fax  +49 941 943 5020
>christian.kohler at klinik.uni-regensburg.de
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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