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

James Carman james at carmanconsulting.com
Wed Sep 22 05:00:40 CEST 2010


So, the "ord" vector contains the indices within
anno$Array_Address_Id_0 where we find the corresponding elements of
featureNames(summary)?

In other words (or symbols):

anno$Array_Address_Id_0[ord[n]] = featureNames(summary)[n]

I hope I have the index notation correct there.

On Tue, Sep 21, 2010 at 10:49 PM, Matthew Ritchie <mritchie at wehi.edu.au> wrote:
> Hi James,
>
> Something like:
>
> anno = read.table("Annotation_Illumina_Human-WG-V3_hg18_V1.0.0_Aug09.txt",
>                   header=TRUE, sep="\t", as.is=TRUE, quote="", fill=TRUE)
>
> ord = match(featureNames(summary), anno$Array_Address_Id_0)
>
> ilmnids = anno$Search_key[ord]
>
> # OR
> ilmnids = anno$Probe_id[ord] # not sure which ILMN_* you require!
>
> should match things up for you.
>
> I assume you are analyzing HT-12 arrays since you have set
> 'imagesPerArray=1'.
>
> Best wishes,
>
> Matt
>
>> 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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>>
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>
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