Adding Unequal Variance to Signature Analysis T-Test #186
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also calculate t-test in figures after filtering tissues
gwaybio
changed the title
cgreene
reviewed
Sep 19, 2019
| @@ -54,7 +54,7 @@ | |||
| " b_activation = feature_series[feature_series.index.isin(group_b_ids)]\n", | |||
| " \n", | |||
| " # Perform t-test on two groups\n", | |||
| " t_stat, t_p = ttest_ind(a_activation, b_activation)\n", | |||
| " t_stat, t_p = ttest_ind(a_activation, b_activation, equal_var=False)\n", | |||
cgreene
reviewed
Sep 19, 2019
| @@ -100,7 +100,7 @@ | |||
| "metadata": {}, | |||
| "outputs": [], | |||
| "source": [ | |||
| "url = \"https://www.nature.com/articles/sdata201733/tables/3\"\n", | |||
| "url = \"https://www.nature.com/articles/sdata201733/tables/4\"\n", | |||
gwaybio
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ef98d58 is the major change of this pull request.
I tracked this error down after failing to align t-test results in subpanels b, d, and f to the results shown in a, c, and e (respectively).
A t-test with equal variance assumption will fail to identify cases found in b.
Another minor change is plotting panels b and d with the test-set features only. Previously, panels a and b were calculated using the test set and panels b and d were generated using the training set. Now, b and d use the test set.
I reran the pipeline after these changes and all files here are updated.
Updated Figure