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

[James Carman]

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