Hi,

Is there a bioconductor package that can read in and analyze methylation data from an illumina iScan scanner? I have the raw data...

thanks!

If you mean the Idat files, then yes. The methylumi (http://bioconductor.org/packages/release/bioc/html/methylumi.html) package can read those data in. There are other packages like minfi that can also use the Idat files (by depending on functions in methylumi).