run harmonypy true_divide error about harmonypy

[gmoore5]

The data that works is literally a subset of this larger set.

So, it seems likely that the larger dataset may have invalid values, and we can avoid the invalid values by taking a subset of the data.

Did you check to see what is inside the adata expression matrix that you're passing to harmony?

Did you check the values of SINGLECELL_TYPE? If there are unused categories, that can be an issue.

If you can provide us with data and code to run on our machines, then we can try to replicate your error and then find a fix.

Hi @slowkow thank you for your response. It was an issue on my end. I didn't realize I was using an older file that did contain missing values. After getting rid of the missing values, I am not getting that error anymore. Sorry about the confusion and I appreciate your willingness to help!

[gmoore5]

Okay so it seems to be an anndata issue since it only happens with this .h5ad file and not others, but I don't know what is different about this dataset versus others? The data that works is literally a subset of this larger set.

[slowkow]

The data that works is literally a subset of this larger set.

So, it seems likely that the larger dataset may have invalid values, and we can avoid the invalid values by taking a subset of the data.

Did you check to see what is inside the adata expression matrix that you're passing to harmony?

Did you check the values of SINGLECELL_TYPE? If there are unused categories, that can be an issue.

If you can provide us with data and code to run on our machines, then we can try to replicate your error and then find a fix.