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

[James Carman]

I guess I'm struggling with how to "match up" (I'm an R newbie) the
ids even if I have the file.  Is there an example somewhere of how to
do this?  I know this is a stupid question, but I am a Java programmer
and I'm just learning R and trying to get my mind around this whole
"everything is a vector" approach. :)

By the way, I tried reading in the manifest file using the readBGX,
but it kept throwing errors, saying something like "link 336 does not
contain 28 elements".

On Tue, Sep 21, 2010 at 8:24 PM, Matthew Ritchie <mritchie at wehi.edu.au> wrote:
> Hi James,
>
> If you just wanted to annotate the probes, this could be done in R using
> the annotation package 'illuminaHumanv3BeadID.db'
>
> If you want to convert the numeric probe IDs to ILMN_* ids, then you can
> use the information in the file
>
> http://www.compbio.group.cam.ac.uk/Resources/Annotation/final/Annotation_Illumina_Human-WG-V3_hg18_V1.0.0_Aug09.zip
>
> (unzip, read in 'Annotation_Illumina_Human-WG-V3_hg18_V1.0.0_Aug09.txt'
> and then match up the probe ids in your summary object with the values in
> the 'Array_Address_Id_0' column.  The corresponding columns in this file
> with ILMN_* ids are either 'Search_Key_0' or 'Probe_Id_0' (entries in both
> start with ILMN_ but end in different numbers - I'm not sure which one you
> are after).  This information can also be obtained from the manifest files
> at
>
> http://www.switchtoi.com/annotationfiles.ilmn
>
> (you will need to select the text version of chip type you are using)
>
> I hope this helps.  Best wishes,
>
> Matt
>
>> 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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