The qc_analysis from bittremieux

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Workflow to analyze the quality of mass spectrometry proteomics experiments based on multivariate quality control metrics.

License: Apache License 2.0

Python 86.45% HTML 5.04% XSLT 8.51%

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Running with the exmaple errors

@bittremieux

Im trying to run the example with the following command:

 python3.4 qc_analysis.py --k_neighbors 2 ../data/qc/PNNL_velos_QuaMeter.tsv ../exampple.html

Im receiving the following error.

Traceback (most recent call last):
  File "qc_analysis.py", line 143, in <module>
    run(parse_args())
  File "qc_analysis.py", line 132, in run
    data = load_metrics(args.file_in, args.min_var, args.min_corr, args.scaling_mode)
  File "qc_analysis.py", line 22, in load_metrics
    data, variance, cor = preprocess.preprocess(data_raw, min_variance=min_var, min_corr=min_corr, scaling_mode=scaling)
  File "/Users/yperez/IdeaProjects/github-repo/BDP/py-pgatk/qc/preprocess.py", line 20, in preprocess
    data, variance = remove_low_variance_features(data, min_variance)
  File "/Users/yperez/IdeaProjects/github-repo/BDP/py-pgatk/qc/preprocess.py", line 31, in remove_low_variance_features
    return data[np.where(variance_threshold.variances_ > min_variance)[0]], variance_threshold.variances_
  File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/pandas/core/frame.py", line 2133, in __getitem__
    return self._getitem_array(key)
  File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/pandas/core/frame.py", line 2177, in _getitem_array
    indexer = self.loc._convert_to_indexer(key, axis=1)
  File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/pandas/core/indexing.py", line 1269, in _convert_to_indexer
    .format(mask=objarr[mask]))
KeyError: '[ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23\n 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 42 43] not in index'

Any advice?

BTW, can you give me a default parameter for this --k_neighbors

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