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cistrome / MIRA

Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
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accessibility model input data must be integers #33

Open yuyanMaggieliu opened 9 months ago

yuyanMaggieliu commented 9 months ago

I encounter this problem when i was running

model = model.set_params(num_topics = 8).fit(data) and the error message is

assert(np.isclose(X.data.astype(np.uint16), X.data, 1e-2).all()), 'Input data must be raw transcript counts, represented as integers. Provided data contains non-integer values.'

my input data was scATAC-seq data, and i don't know why it triggers that error

AllenWLynch commented 6 months ago

Please check the data in your AnnData object. Perhaps some of the values are not integers, like if a CPM transformation was applied!