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

Christian Kohler Christian.Kohler at klinik.uni-regensburg.de
Tue Mar 18 16:34:49 CET 2008

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

More information about the Bioconductor mailing list