[BioC] Read .idat Illumina files in R

[Moiz Bootwalla]

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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