Unfortunately, this won't help for expression arrays.  Last time I checked,
those IDATs appeared to be encrypted.

crlmm, methylumi, and minfi can all read IDAT files... *if* they are
"version 3" or later (e.g. genotyping, methylation, etc).

Otherwise you are probably stuck with GenomeStudio if it is expression data
you're dealing with.

On Wed, Apr 11, 2012 at 7:14 AM, Moiz Bootwalla <msbootwalla@gmail.com>wrote:

> Hi Ekta,
>
> You can use the bioconductor package methylumi to read in .idat files. The
> function methylumIDAT() will read in .idat files and provide you with beta
> values along with the M and U values as a MethyLumiSet object. You can then
> use the functions methylumi.bgcorr() and normalizeMethyLumiSet() to
> background correct and normalize your data. See the vignette for more
> details.
>
> Best,
> Moiz
>
>
> On Apr 11, 2012, at 1:46 AM, Ekta Jain wrote:
>
> > Dear Bioc and R List Users,
> > I am having trouble analysing illumine data generated from BeadScan. I
> have .idat files and JPEG images. I realise that i need bead-level summary
> data to be able to begin quality control followed by normalization. Is
> there a way i can read .idat files for expression analysis or do i need to
> go back to BeadScan and generate .txt files/tiff files ?
> >
> > Appreciate any help here.
> >
> > Many Thanks,
> > Ekta Jain
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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