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

Matthew Ritchie mritchie at wehi.EDU.AU
Wed Sep 22 02:24:44 CEST 2010

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


(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


(you will need to select the text version of chip type you are using)

I hope this helps.  Best wishes,


> I am trying to get a summarized table from our Illumina data.  So far I
> targets = read.table("/home/jcarman/targets.txt", header=TRUE,
as.is=TRUE) detail =
> readIllumina(arrayNames=targets$Id,useImages=FALSE,annoPkg="Humanv3",targets=targets)
> 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
> 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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