Running Forebrain turorial

[Pacomito]

Hi @jsxlei ! Thanks for the nice tool & article, I would like to try out your tool, the installation step worked fine but running the tutorial I came across an error :

python3.6 SCALE.py -d Forebrain/data.txt -k 8 --impute

Loading data ... Original data contains 2088 cells x 678 peaks Finished loading takes 0.00 min /usr/local/lib/python3.6/dist-packages/scipy/sparse/compressed.py:213: RuntimeWarning: invalid value encountered in greater res = self._with_data(op(self.data, other), copy=True) /usr/local/lib/python3.6/dist-packages/scipy/sparse/compressed.py:213: RuntimeWarning: invalid value encountered in greater res = self._with_data(op(self.data, other), copy=True) Traceback (most recent call last): File "SCALE.py", line 77, in transpose=args.transpose, transforms=[normalizer.fit_transform]) File "/home/pprompsy/SCALE-master/scale/dataset.py", line 42, in init self.data = transform(self.data) File "/usr/local/lib/python3.6/dist-packages/sklearn/base.py", line 553, in fit_transform return self.fit(X, **fit_params).transform(X) File "/usr/local/lib/python3.6/dist-packages/sklearn/preprocessing/data.py", line 907, in fit return self.partial_fit(X, y) File "/usr/local/lib/python3.6/dist-packages/sklearn/preprocessing/data.py", line 926, in partial_fit force_all_finite='allow-nan') File "/usr/local/lib/python3.6/dist-packages/sklearn/utils/validation.py", line 558, in check_array context)) ValueError: Found array with 0 feature(s) (shape=(1, 0)) while a minimum of 1 is required by MaxAbsScaler.

Thanks in advance, Pacome

[jsxlei]

Hi Pacome, The Forebrain dataset provided is supposed to contain 2088 cells x 11286 peaks (double checked), but your post info said your input data is 2088 cells x 678 peaks, I think it maybe the input data has not completely downloaded, please check out the input data. Lei

[Pacomito]

Thanks @jsxlei, yes it seems that the download didnt finished, I will try again and let you know, Cheers

[Pacomito]

It all works fine, Thanks again