If you're using Mark Dunning's package, you should...

library(illuminaHumanv4.db)
conn <- illuminaHumanv4_dbconn()
sql <- 'SELECT ReporterGroupName, COUNT(ArrayAddress) AS probes
               FROM ExtraInfo GROUP BY ReporterGroupName'

dbGetQuery(conn, sql)
## data frame with 100 rows and 2 columns
##              ReporterGroupName    probes
##                    <character> <integer>
## 1                           NA     47224
## 2                   ERCC-00002         1
## 3                   ERCC-00003         1
## 4                   ERCC-00004         1
## 5                   ERCC-00009         1
## ...                        ...       ...
## 96  cy3_hyb,low_stringency_hyb         4
## 97                housekeeping         7
## 98                    labeling         2
## 99          low_stringency_hyb         4
## 100                   negative       770

Whether the resulting mapped probes get put into the right place in a given
data structure is another matter...



*He that would live in peace and at ease, *
*Must not speak all he knows, nor judge all he sees.*

Benjamin Franklin, Poor Richard's
Almanack<http://archive.org/details/poorrichardsalma00franrich>


On Thu, Nov 28, 2013 at 1:53 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> I agree here that having packages maintain their own routines probably
> makes sense.  What I am not clear on yet is if we have all the annotation
> to account for the various control probes.  Does anyone know?
>
> Sean
> Hi Gordon,
>
> Matt has kindly already sent me a copy of his script for creating the EList
> object.  Combined with Sean's code for generating a LumiBatch and the
> script I'm putting together for beadarray I think we have most of the
> downstream expression analysis packages covered.  My initial hope was that
> individual packages would import illuminaio (I like the elegance of having
> a single function in the library) and modify their data input routines to
> take both the text and IDAT formats.  I'll discuss it with Kasper as
> illuminaio is ultimately his package.
>
> Cheers,
>
> Mike
>
>
> On 28 November 2013 02:20, Gordon K Smyth <smyth@wehi.edu.au> wrote:
>
> > Dear Sean and Mike,
> >
> > We (actually Matt Ritchie) have written a nice little function that uses
> > readIDAT() to read the IDAT files and assembles the pieces into a data
> > object ready for limma analysis.  The output is an EList object, but it
> > could be an ExpressionSet instead.
> >
> > It has been suggested that this function could be added to the limma
> > package, but I wondered whether the illuminaio package would be the best
> > home.
> >
> > What would you like us to do?
> >
> > Best wishes
> > Gordon
> >
> >  Date: Tue, 26 Nov 2013 09:33:17 -0500
> >> From: Sean Davis <sdavis2@mail.nih.gov>
> >> To: "bioconductor@r-project.org" <bioconductor@r-project.org>
> >> Subject: [BioC] Illumina Expression analysis from iDAT files
> >>
> >> Hi, all.
> >>
> >> I have a set of iDAT files from illumina expression arrays and have been
> >> looking around for a workflow that begins with the iDAT files.
>  Illuminaio
> >> can read them and beadarray and lumi packages (to name a couple) can
> deal
> >> with illumina data normalization and processing, but I didn't find a
> >> bridge
> >> between the illuminaio output and further processing.  I very well may
> >> have
> >> missed something, but I thought I would check.
> >>
> >> Thanks,
> >> Sean
> >>
> >
> > ______________________________________________________________________
> > The information in this email is confidential and inte...{{dropped:12}}
>
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