I can't think of any reason why the number of matrices would be limited to 1000. There is no limit imposed in the code. 

Perhaps this is a memory issue... 

Originally posted by liam nestor:

I have thousands of matrices (~5000) as inputs in order to perform unpaired t-tests. I have been experimenting with smaller samples to begin with ( ~700) and NBS runs without problems. As soon as the number goes beyond 1000 matrices as inputs I get a message about the design matrix not being found or inconsistent. I'm updating the design matrix to align with the number of matrices inputs, so I don't understand. Any ideas why this might be happening? All the best, Liam.