[R] [BioC] Read .idat Illumina files in R

[grimbough]

I posted this to BioC yesterday, but I'll include it here for completeness:  

The expression array idats are indeed encrypted.  However you can read them
using the package available here:

http://www.compbio.group.cam.ac.uk/Resources/IDATreader/

You can get back a data.frame containing the summarized intensity values for
all bead types, along with values such as the number of beads of each type,
the standard deviation with and without outliers etc.

Note that this isn't the same as bead-level data.  If that wasn't generated
at the time of the scan there's nothing that you can do to get it from the
idats and jpegs.

Mike


Tim Triche, Jr. wrote
> 
> 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.
> 


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