CODEWITHSUNDEEP
pythonscipy
ytrewq
ytrewq

Reputation: 3930

python scipy stats module: ValueError: 'axis' entry is out of bounds

I'm using scipy's stats to calculate Fisher's Exact Test score.. It works perfectly fine, except for some matrices, it returns valueError. For example,

odds, pvalue = stats.fisher_exact([[1,2],[9,84419233]])

returns

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Python/2.7/site-packages/scipy-0.14.0.dev_4938da3-py2.7-macosx-10.8-x86_64.egg/scipy/stats/stats.py", line 2606, in fisher_exact
    if float(np.abs(pexact - pmode)) / np.abs(np.max(pexact, pmode)) <= 1 - epsilon:
  File "/Library/Python/2.7/site-packages/numpy-1.9.0.dev_fde3dee-py2.7-macosx-10.8-x86_64.egg/numpy/core/fromnumeric.py", line 2126, in amax
    return amax(axis=axis, out=out)
  File "/Library/Python/2.7/site-packages/numpy-1.9.0.dev_fde3dee-py2.7-macosx-10.8-x86_64.egg/numpy/core/_methods.py", line 17, in _amax
    out=out, keepdims=keepdims)
ValueError: 'axis' entry is out of bounds

I have no idea why this shouldn't work..

Could someone please help me out?

Upvotes: 1

Views: 1090

Answers (1)

Warren Weckesser
Warren Weckesser

Reputation: 114811

This is a bug in the fisher_exact function. I've reported the problem here: https://github.com/scipy/scipy/issues/3014

Upvotes: 1

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