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

[Christian Kohler]

Hi Mark and Jenny,

thanks a lot for your detailed answers.
After heeding your advice, I now understand :-)

Best,
Christian

Mark Dunning wrote:
> 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 This script was a bit outdated I'm afraid.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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>


-- 

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