Loading 450k methylation data as follows:
methyset <- methylumIDAT(barcodes=barcodes, parallel=TRUE, idatPath="./data/IDATS")
Then the following code will error (subscript out of bounds):
This is because there are only 850 QC probes, which should not be subset with the indices used on the main dataset.
The code responsible is below: https://github.com/Bioconductor-mirror/methylumi/blob/master/R/MethyLumiSet-class.R#L454