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oist / optinist

calcium imaging pipeline tool
GNU General Public License v3.0
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PCA issue #591

Open milesOIST opened 7 months ago

milesOIST commented 7 months ago

Issue running PCA on example data File "...optinist/core/nwb/nwb_creater.py", line 375, in set_nwbconfig nwbfile = NWBCreater.column( TypeError: column() got an unexpected keyword argument 'discription' Same issue with TSNE

milesOIST commented 7 months ago

rerunning I now get this issue line 146, in _assert_all_finite raise ValueError(msg_err) ValueError: Input X contains NaN. PCA does not accept missing values encoded as NaN natively. For supervised learning, you might want to consider sklearn.ensemble.HistGradientBoostingClassifier and Regressor which accept missing values encoded as NaNs natively. Alternatively, it is possible to preprocess the data, for instance by using an imputer transformer in a pipeline or drop samples with missing values. See https://scikit-learn.org/stable/modules/impute.html You can find a list of all estimators that handle NaN values at the following page: https://scikit-learn.org/stable/modules/impute.html#estimators-that-handle-nan-values