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Differential-expression analysis using logistic regression in Seurat - glm.fit warning message

Hi,

I am performing differential-expression analysis in Seurat using the logistic regression test with "donor" as a latent variable. While it does give me an output, I am getting the following warning message.

Warning message:
glm.fit: fitted probabilities numerically 0 or 1 occurred

What does this mean and should I be concerned about it?

Many thanks,

Lucy

scrna-seq seurat differential-expression analysis
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updated by jared.andrews07 jared.andrews07 • written by Lucy • Lucy

1 answer

This crossvalidated question answers this quite well. In short, this is likely due to certain genes having no counts in certain donors leading to perfect separation for that variable (which in most cases is odd to see in logistic regression, hence the warning) and can (probably) be ignored safely.

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written by jared.andrews07 jared.andrews07

Ah great, thank you.

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written by Lucy • Lucy

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