Thanks, Mike, for the confirmation and for the continued work on this
stuff.  I wrote a quick little function that uses illuminaio readIDAT and
generates a LumiBatch from the lumi package.  The function doesn't have any
bells-and-whistles, but it will suffice for me right now.

https://gist.github.com/seandavi/7661290

Sean



On Tue, Nov 26, 2013 at 10:07 AM, Mike Smith <grimbough@gmail.com> wrote:

> Hi Sean,
>
> The short answer is that you are correct, there isn't currently a quick and
> easy way to read IDAT files into R and then feed the data to downstream
> processing packages. The inclusion of the expression IDAT reading routines
> in illuminaio is still fairly new compared to the support for other
> platforms.
>
> My hope is for downstream packages to use the reading routines from
> illuminaio directly, in a similar fashion to crlmm and minfi.  I'm
> currently working on implementing this for beadarray.  As a short fix you
> can use illuminaio to generate a text file similar to the output from
> GenomeStudio, but this isn't a very satisfactory solution.
>
> Let me know if you run into any difficulties, the expression reading code
> has not been that widely used.
>
> Cheers,
> Mike Smith
>
>
> On 26 November 2013 14:33, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> > 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
> >
> >         [[alternative HTML version deleted]]
> >
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> >
>
>
>
> --
> Mike Smith
> Research Associate
> Statistics & Computational Biology Laboratory
> Cambridge University
>
>         [[alternative HTML version deleted]]
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