It depends on memory (RAM) installed in your computer. Though it's difficult to say an exact number, the tentative limitations per series on 4GB RAM box are like this.
- ~ 100 samples with 25,000 probes.
- ~ 50 samples with 50,000 probes.
- ~ 10 samples with 250,000 probes.
But we don’t recommend you try upper limits, because the system gets unstable and erroneous when it's running short of memory. If you want to analyze a large data set, please use a computer with large memory (8 - 64 GB).
Performance is another issue. For better performance, high-spec machine with faster CPU and Soled State Drive (SSD) is the solution.