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): methyset[1:1000, 1:2]

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

Thanks for the report. This should be fixed in 2.24.1 (release) and 2.25.1 (devel) versions.