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We can more easily automate tests via setup.py with "python setup.py test" using [setuptools](http://pythonhosted.org/an_example_pypi_project/setuptools.html).
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Multiple comparisons corrections with something like Bonferroni would be useful. This would also require generating p-values for the logrank statistic from the Chi**2 distribution.
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To both tables add columns with the modified P value:
- Bonferonni/Hall correction (the smallest P values \* number of symptoms; the second smallest P value \* number of symptoms-1; etc;) Sort sympto…
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When I am testing the NULL reference constraint, I sometimes get this error:
```
Caused by: org.intermine.objectstore.ObjectStoreQueryDurationException: Estimated time to run query(25557935522) great…
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Hi,
After running find_enrichment.py I just wonder whether it is possible to know which Gene ID has been used for each line of the below results?
id enrichment description ratio_in_stud…
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Hi,
I tried the option --compare with the following comand:
```
$ python scripts/find_enrichment.py --compare --indent data/study data/population data/association
```
and got the following error…
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It looks like the nosetests are succeeding on travis-ci but the script still exits with a 1, causing a failure:
https://travis-ci.org/SimTk/openmm
Any ideas on how to fix this?
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Hi,
First of all, thank you very much for the scritps. They are very useful and easy to use.
I was wondering if there is any way to get all GO terms analysed, regardless alpha values.
That is, woul…
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Hello,
What the dots mean before the GO terms?
```
python scripts/find_enrichment.py --alpha=0.05 --fdr --indent data/study data/population data/association
id enrichment description ratio…
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degree of freedom bug:
compare_alpha_diversity.py relies on passing flattened matrices to the t_two_sample test in cogent/maths/stats/test.py. the way degrees of freedom are calculated is based on th…