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

[Matthew Ritchie]

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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