I am trying to run a script for data processing (https://github.com/allanjust/methylation-lab/blob/master/code/meth01_process_data.R) of Infinium MethylationEPIC BeadChip (Illumina) data. However, I am unable to run the preprocessing step of the RGChannelSet (WB) using the preprocessNoob function (minfi package) and gets following error:
preprocessNoob(WB) Error in huber(controls[, i]) : cannot estimate scale: MAD is zero for this sample
I have removed one of the samples from the RGChannelSet which failed to pass all the control parameters (NaN or Infinity) from the BeadArray Controls Reporter software. However, it did not affect the error.
Any suggestions for solving the issue?
Thank you, Steffan