I am using the steps in the vignette to analyze my data. When I attempted Section 5, I received the following errors while using ExomeDepth's command: 

 > my.choice <- select.reference.set (test.counts = my.test, reference.counts = my.reference.set, bin.length = (ExomeCount.dafr$end - ExomeCount.dafr$start)/1000, n.bins.reduced = 10000)

Optimization of the choice of aggregate reference set, this process can take some time
It looks like the test samples has only 2 bins with 2 or more reads. The coverage is too small to perform any meaningful inference so no likelihood will be computed.

OR the next error message: 

Optimization of the choice of aggregate reference set, this process can take some time
Error in select.reference.set(test.counts = my.test, reference.counts = my.reference.set,  :
The number of rows of the reference matrix must match the length of the test count data

Does anyone know how to set up the my.test and my.ref.samples so these messages don't pop up?

I've tried a 1 to 1 correspondence between reference and test samples, but its either too little or so many

that it causes the second error.

Thanks in advance!