[BioC] Pulling significant gene ids from beadarray data

[Johnstone, Alice]

I have been analysing my Illumina data from rat ref12 using beadarray
and the summary data.  I have managed to get a list of significantly
different probes, but am at a loss as to how to get the gene info this
corresponds to. The ExpressionSetIllumina object doesn't contain any
annotation data, neither the ProbeID or the TargetID appear to be
incorporated following the code in the vignette (march 26 2007).  Is
there a way to include this to ensure I am following the right probe?
Then is there a way to get the gene information directly to R, such as
when using the lumi package and nuID etc?
Any help gratefully appreciated! 

Alice Johnstone
PhD Candidate
Institute of Environmental Science and Research Ltd
Kenepuru Science Centre
34 Kenepuru Drive
PO Box 50-348
Porirua
New Zealand
Tel:  + 64 4 914-0717
Fax: + 64 4 914-0770

dataFile="ROD-AJ-BeadStudioV2_Sample_Probe_Profile.csv"
qcFile="ControlGeneProfile.csv"
sampleSheet="sampleSheet.csv"
BSData<-readBeadSummaryData(dataFile,qcFile=qcFile,sampleSheet=sampleShe
et,
header=TRUE,skip=7,columns=list(exprs="AVG_Signal",BeadStDev="BEAD_STDEV
",
NoBeads="Avg_NBEADS"),qc.columns=list(exprs="AVG.Signal",Detection="Dete
ction"),
qc.skip=0,qc.sep=",",sep=",")

> exprs(BSData)[1:10,1:2]
     SAL SAL.1
1  151.8 151.2
2  142.6 133.4
3  143.6 151.0
4  135.6 138.2
5  149.5 153.6
6  133.1 155.1
7  141.2 157.4
8  144.2 135.4
9  168.0 132.7
10 126.5 144.7 


> sessionInfo()
R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 
 
locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_MONETARY=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
 
attached base packages:
[1] "grid"      "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets"  "methods"   "base"     
 
other attached packages:
   beadarray beadarraySNP  quantsmooth      lodplot     quantreg
SparseM         affy       affyio  geneplotter 
     "1.4.0"      "1.2.0"      "1.2.0"        "1.1"       "4.08"
"0.73"     "1.14.2"      "1.4.1"     "1.14.0" 
     lattice     annotate      Biobase        limma 
   "0.15-11"     "1.14.1"     "1.14.1"     "2.10.5"