Proseg estimated counts

[jairaj-mathur]

Hi @dcjones

Proseg 3.1 is looking good! I had a conceptual question regarding the proseg estimated counts.

These are the counts that I get in my zarr object, right? Is there another set of counts that are also generated? The resolvi scverse discussions talk about using proseg estimated counts for clustering, and I was wondering if there is anything different to do to get those.

Warm regards

Jairaj Mathur

[dcjones]

Hi @jairaj-mathur

There are two kinds of count matrix estimates it can produce. By default you get a normal estimate of integer counts, but you can also separately output an expected count matrix with --output-expected-counts ecounts.mtx, which is an average over a bunch of samples.

Many versions ago proseg would only output this expected count matrix, but this proved to be annoying because many downstream analyses assume a matrix of integers, so that behavior was changed at some point.