[BioC] Illumina Expression analysis from iDAT files

Gordon K Smyth smyth at wehi.EDU.AU
Thu Nov 28 03:20:01 CET 2013

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 

What would you like us to do?

Best wishes

> Date: Tue, 26 Nov 2013 09:33:17 -0500
> From: Sean Davis <sdavis2 at mail.nih.gov>
> To: "bioconductor at r-project.org" <bioconductor at 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 intend...{{dropped:4}}

More information about the Bioconductor mailing list