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jsxlei / SCALE

Single-cell ATAC-seq analysis via Latent feature Extraction
MIT License
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UserWarning Issues #13

Closed cartal closed 4 years ago

cartal commented 4 years ago

Hi,

I'm running SCALE on 55K cells and I'm getting the following warnings: 

UserWarning: Numerical issues were encountered when scaling the data and might not be solved. Dataset may contain too large values. You may need to prescale your features.

and

UserWarning: Numerical issues were encountered when scaling the data and might not be solved. The standard deviation of the data is probably very close to 0.

It ultimately fails with:

ValueError: Input contains NaN, infinity or a value too large for dtype('float32').

My questions are:

1) How do you propose to pre-scale my data?

2) Do you have some diagnostics steps on why this may be?

Thanks!