you don't say which array you are using so full details can't be provided,
but one approach for human arrays is

> library(lumiHumanAll.db)
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: org.Hs.eg.db
Loading required package: DBI
> library(annaffy)
Loading required package: GO.db
Loading required package: KEGG.db

> pr = mappedkeys(lumiHumanAllENTREZID)
> length(pr)
[1] 46237
#
# i find the full mapping is slow, but for 50 probes:
#
> afm = aafTableAnn(pr[1:50], "lumiHumanAll.db")
> saveHTML(afm, file="~/afm.html")
#
# now point browser to ~/afm.html
#
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-05-03 r51901)
x86_64-apple-darwin10.3.0

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
 [1] annaffy_1.21.0         KEGG.db_2.4.1          GO.db_2.4.1
 [4] lumiHumanAll.db_1.10.0 org.Hs.eg.db_2.4.1     RSQLite_0.9-0
 [7] DBI_0.2-5              AnnotationDbi_1.11.1   Biobase_2.9.0
[10] weaver_1.15.0          codetools_0.2-2        digest_0.4.2


On Mon, May 17, 2010 at 4:31 AM, Taylor, Katie <kt70@leicester.ac.uk> wrote:

> Hello,
>
> I hope that you can help me. I am looking for a way to make a hyperlink
> table/html document which contains the annotation and data of my illumina
> microarray. Does anyone know if this can be done? I have found functions
> where I can look up a range or individual set of genes but I need the whole
> table. I've been using annaffy for some geo data that I downloaded but I was
> wondering if somthing like this could also be used for illumina? The nuID
> conversion is what makes me think that annaffy can't be used but I can't
> find anything in lumi which will do what I need. I would be really grateful
> of any help that you could give me.
>
> Best Wishes,
>
> Katie
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