I have tried Methylkit with many datasets and it always worked well using the function calculateDiffMethDSS.
However, I am trying to run a data set with no replicates and it crashed when running calculateDiffMethDSS. It returns the error:
Error in rowMeans(p) : 'x' must be an array of at least two dimensions
The same data set works well using calculateDiffMeth instead of calculateDiffMethDSS.
Do you have any ideas why? Could it be because that there are no replicates?
Please, let me know if you need more information.