scanpy Fixup #566 & #706

I think the reason of issues(#566 & #706) is that the value of xyz in sqrt(xyz) is too large and overflow encountered in long_scalars. After updating these codes, the ValueError disappeared in my PC.

Dec 12 '19 08:12 QuarkFang

#530 also related. Are you including the log_transformed=True kwarg in your call to rank_genes_groups()?

Dec 17 '19 22:12 chmreid

#530 also related. Are you including the log_transformed=True kwarg in your call to rank_genes_groups()?

oh, I'm not. But when I included it, the ’ValueError: math domain‘ error still appeared.

Dec 19 '19 08:12 QuarkFang

In #706 @LuckyMD gives a minimal working example in this comment that may give you a useful starting point. Their advice to create/post a way to reproduce the error is good too, as it may help you identify the source of the problem in the process (and make it easier for others to help troubleshoot)!

Dec 19 '19 18:12 chmreid

Unfortunately I am still facing this problem! Is there a way to avoid it?

Apr 09 '20 01:04 bioguy2018