Sigma is not positive definite in mvnorm() call about scdesign2 HOT 4 CLOSED

Hi,

While running scDesign2 I received the following error:

The actual counts I used as input to scDesign2 were obtained from the Mouse Olfactory Bulb dataset from the following:
https://www.spatialresearch.org/resources-published-datasets/doi-10-1126science-aaf2403/

I was wondering if there is a way to resolve this issue?

Hi Andrew,

Thank you for bringing this to our attention. Could you be a little bit more specific about how this issue came up? For example, I can see 12 replicate datasets plus 4 "layer" datasets in the link provided. Which count matrix did you use that gave rise to this issue? And did you filter for genes, perform any clustering or any value transformation? If you can provide the code that you used, It will be very helpful.

Best,
Tianyi

from scdesign2.

Hi Tianyi,

Thank you for getting back to me. As of now, I need to isolate which replicate caused the issue. I will reply again once I can replicate the issue with more details.

Best,
Andrew

from scdesign2.

Hi Tianyi,

Thank you for getting back to me. As of now, I need to isolate which replicate caused the issue. I will reply again once I can replicate the issue with more details.

Best,
Andrew

Sounds good!

from scdesign2.

Hi Tianyi,

I tried again to replicate the error on Linux, but I was unable to. Thank you for your assistance.

Best,
Andrew

from scdesign2.