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highly_variable_genes not working for normalized values from edgeR::cpm #43

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dweemx opened this issue Apr 17, 2020 · 0 comments · Fixed by vib-singlecell-nf/vsn-pipelines#204
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highly_variable_genes not working for normalized values from edgeR::cpm #43

dweemx opened this issue Apr 17, 2020 · 0 comments · Fixed by vib-singlecell-nf/vsn-pipelines#204
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dweemx commented Apr 17, 2020

For some reason, the highly_variable_genes from scanpy is not working for normalized (log + CPM) matrix coming from edgeR. Not setting min_mean, max_mean, min_disp, max_disp will lead to no variable genes detected.
image

It seems that it's due to max_mean. By setting it to a number (in the range of the values) or np.inf, the function seems to work fine. I haven't got time exactly to know why.
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@dweemx dweemx added the bug Something isn't working label Apr 17, 2020
@dweemx dweemx self-assigned this Apr 17, 2020
@dweemx dweemx changed the title highly_variable_genes not working for normalized values highly_variable_genes not working for normalized values from edgeR::cpm Apr 17, 2020
dweemx added a commit that referenced this issue Apr 17, 2020
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Fix #43
c837b65
@dweemx dweemx mentioned this issue Apr 17, 2020
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