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. > -- View this message in context: http://r.789695.n4.nabble.com/Read-idat-Illumina-files-in-R-tp4548360p4555147.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
