Hi Dick,

Sorry for taking a while to get back to you.  Section 9 of the bead-level
vignette covers how to get summary data  from bead-level data:
http://www.bioconductor.org/packages/2.8/bioc/vignettes/beadarray/inst/doc/beadlevel.pdf

The first 4 lines from the examples code in that section will create an
ExpressionSetIllumina object using the default summarisation parameters,
which is what you would get if you read summary data directly into
beadarray.

Personally I find the need to set up the channels (the first 3 lines of the
example) a bit confusing, so if you're using the developmental version of
beadarray (currently version 2.3.7) we've sorted the defaults out so you can
simply type:

summarize(BLData)

to get the summary data.

I hope that's some help,

-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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