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

[Lynn Amon]

One problem here is that Illumina keeps changing their naming schemes
both with new versions of the arrays and with new versions of
BeadStudio.  In the next release of the Illumina annotation files, I
will include versions that are based on the ProbeID which I understand
BeadStudio is now calling Array_Address.  You can process files written
out by the scanner software (BeadScanner) directly without using
BeadStudio which use the ProbeID as the identifier so this should remain
constant regardless of changes made to BeadStudio.  These are the .csv
and .txt files.  The latter includes an entry for every probe type and
is quite large.  I recommend using the summarized version in the .csv
format.  I will also include a version based on the TargetID which may
now be called ILMN_Gene.  I believe the ProbeIDs are unique. 
Lynn Amon


Jenny Drnevich wrote:
> 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.
>
> Cheers,
> Jenny
>
> 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)
>> 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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>>     
>
> 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
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
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