3.6 years ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
The function read.idat() is now provided in the limma package to read idat files. So you no longer need to export a text file from Genome Studio.
The function read.idat() is a new addition to the limma package and is not yet described in the limma User's Guide, which describes only how to the read exported text files from Genome Studio. The new function reads Illumina's encrypted binary IDAT files directly using the capabilities of the illuminio package.
To read and normalize the data:
x <- read.idat(idatfiles, bgxfile)
y <- neqc(data)
where 'idatfiles' and 'bgxfile' are the names of the IDAT and BGX files. Then 'y' can be input directly to lmFit(). You can follow the case study in Section 17.3 of the limma User's Guide, except that read.idat() replaces read.ilmn().