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Mean expression can be negative in _get_perturbation_markers #684

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Zethson opened this issue Dec 10, 2024 · 0 comments
Open

Mean expression can be negative in _get_perturbation_markers #684

Zethson opened this issue Dec 10, 2024 · 0 comments
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@Zethson
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Zethson commented Dec 10, 2024

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A kind user: When I examined the function _get_perturbation_markers, I noticed that the mean expression for some groups could be negative, resulting in an invalid Log2FC value (NaN). This negative mean seems to arise from subtracting the expression values of genes in the Perturb-sample cell from the averaged expression of its 20 nearest neighbor cells in the Control sample.

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@Zethson Zethson added the bug Something isn't working label Dec 10, 2024
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