[BioC] [beadarray] Converting Probe IDs to ILMN Gene Names...

[James Carman]

What do you mean by "feed"?  I passed in the annoPkg="Humanv3"
parameter.  What else do I have to do?

On Tue, Sep 21, 2010 at 7:24 PM, Tim Triche <tim.triche at gmail.com> wrote:
> have you fed beadarray a bead ID annotation package?
> http://bioconductor.org/packages/2.6/data/annotation/html/illuminaHumanv3BeadID.db.html
> I didn't see one in your sessionInfo()
>
>
> On Tue, Sep 21, 2010 at 11:39 AM, James Carman <james at carmanconsulting.com>
> wrote:
>>
>> I am trying to get a summarized table from our Illumina data.  So far I
>> have:
>>
>> targets = read.table("/home/jcarman/targets.txt", header=TRUE, as.is=TRUE)
>> detail =
>> readIllumina(arrayNames=targets$Id,useImages=FALSE,annoPkg="Humanv3",targets=targets)
>> summary=createBeadSummaryData(detail,imagesPerArray=1,method="illumina")
>>
>> How do I get the probe ids mapped to the ILMN_* gene ids for my output?
>>
>> sessionInfo() returns:
>>
>> R version 2.11.1 (2010-05-31)
>> x86_64-redhat-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] beadarray_1.16.0 Biobase_2.8.0
>>
>> loaded via a namespace (and not attached):
>> [1] hwriter_1.2  limma_3.4.4  tools_2.11.1
>>
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>
>
>
> --
> With four parameters I can fit an elephant, and with five I can make him
> wiggle his trunk.
> John von Neumann
>