Hello pydeseq2 devs.
Thank you all for developing this easy-to-use analysis tool. I'm running into extremely long runtimes (or possibly just hanging) when running dds.fit_genewise_dispersions(). I've seen some chatter about similar issues in the past when running dds.deseq2().
As others have pointed out, this issue appears linked to occurences of 0 within the matrix. Adding 1 to all counts seems to resolve the issue, but I'd prefer to avoid this if possible.
Does anyone have practical advice for working around this issue?
Hello pydeseq2 devs.
Thank you all for developing this easy-to-use analysis tool. I'm running into extremely long runtimes (or possibly just hanging) when running dds.fit_genewise_dispersions(). I've seen some chatter about similar issues in the past when running dds.deseq2().
As others have pointed out, this issue appears linked to occurences of 0 within the matrix. Adding 1 to all counts seems to resolve the issue, but I'd prefer to avoid this if possible.
Does anyone have practical advice for working around this issue?