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
>>
>
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