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

[Mark Dunning]

Hi Christian,

This script was a bit outdated I'm afraid. The package was recently  
changed so that it would use the ProbeID column in the input files to  
give a unique row name in the resulting ExpressionSet. Unfortunately,  
the file provided with the package did not have this column, hence R  
gives an error when we try and assign a vector of length 0 to the  
names of a matrix.

If you add the argument ProbeID= "TargetID" to readBeadSummaryData it  
should work. Thanks to Vince Carey for also pointing this error out  
and the solution.

There is also a problem in the code where we try and use BiomaRT to  
get information about a set of probes. The vector illuids passed to  
getBM is never defined. However, if you set to something appropriate  
(maybe the rownames of the topTable output) then this command should  
work fine also.

I will update the script shortly with these changes.

Hope this helps,

Mark




On 18 Mar 2008, at 15:34, 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)
> x86_64-unknown-linux-gnu
>
> locale:
> C
>
> 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.
>
> Cheers
> Christian
>
>
>
>
> -- 
>
> 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
>
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