I am getting following error related to read.metharray, while running my Script,

Error in read.metharray(basenames = files, extended = extended, verbose = verbose,  : 
  !anyDuplicated(basenames) is not TRUE

FYI, I made my sample sheet on my own by removing the information of some of the samples for which the data was missing. I have double checked that now my meth_idat folder has exactly the same number of samples each with 2 idat files as mentioned in my sample sheet. But still getting this error.

Any help will be highly appreciated.

Thanks

If you're using read.metharray, the base names argument is a vector which is half the length of the number of files, equal to the number of samples. You need to remove the _Grn and _Red from the file names and remove any duplicates.

read.metharray.exp() is probably an easier to use interface.