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glasgowcompbio / PALS

Ranking metabolite (and other omics sets) by their activity levels via SVD
https://pals.glasgowcompbio.org
MIT License
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Suspicious warning #2

Open joewandy opened 4 years ago

joewandy commented 4 years ago 
2019-11-15 10:41:02.602 | DEBUG    | pals.pathway_analysis:_change_zero_peak_ints:248 - Setting the zero intensity values in the dataframe
2019-11-15 10:41:02.667 | DEBUG    | pals.pathway_analysis:_standardize_intensity_df:228 - Scaling the data across the sample: zero mean and unit variance
2019-11-15 10:41:02.709 | DEBUG    | pals.pathway_analysis:get_plage_activity_df:67 - Mean values of the rows in the DF is [-0. -0. -0. ...  0. -0.  0.]
2019-11-15 10:41:02.709 | DEBUG    | pals.pathway_analysis:get_plage_activity_df:68 - Variance in the rows of the DF is [0. 0. 0. ... 0. 0. 0.]
2019-11-15 10:41:03.704 | INFO     | pals.pathway_analysis:set_up_resample_plage_p_df:79 - Calculating plage p-values with resampling
2019-11-15 10:41:03.705 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:83 - Comparison Distal_vs_Proximal
2019-11-15 10:41:03.705 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 0/1000
..\pals\pathway_analysis.py:313: RuntimeWarning: invalid value encountered in true_divide
  tvalues = (m1 - m2) / se_total
2019-11-15 10:41:03.806 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 100/1000
2019-11-15 10:41:03.899 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 200/1000
2019-11-15 10:41:03.995 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 300/1000
2019-11-15 10:41:04.092 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 400/1000
2019-11-15 10:41:04.187 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 500/1000
2019-11-15 10:41:04.283 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 600/1000
2019-11-15 10:41:04.380 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 700/1000
2019-11-15 10:41:04.478 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 800/1000
2019-11-15 10:41:04.574 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:91 - Resampling 900/1000
2019-11-15 10:41:04.672 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:97 - Total time 0
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py:901: RuntimeWarning: invalid value encountered in less
  return (a < x) & (x < b)
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py:1892: RuntimeWarning: invalid value encountered in less_equal
  cond2 = cond0 & (x <= _a)
2019-11-15 10:41:04.930 | INFO     | pals.pathway_analysis:_calculate_coverage_df:333 - Calculating dataset formula coverage
2019-11-15 10:41:04.932 | INFO     | pals.pathway_analysis:calculate_hg_values:158 - Calculating the hyper-geometric p-values
2019-11-15 10:41:05.119 | INFO     | pals.pathway_analysis:calculate_hg_values:190 - Calculating the combined p-values
joewandy commented 4 years ago

More suspicious warning

2019-11-25 12:00:37.734 | DEBUG    | pals.pathway_analysis:_change_zero_peak_ints:250 - Setting the zero intensity values in the dataframe
2019-11-25 12:00:37.813 | DEBUG    | pals.pathway_analysis:_standardize_intensity_df:230 - Scaling the data across the sample: zero mean and unit variance
2019-11-25 12:00:37.842 | DEBUG    | pals.pathway_analysis:get_plage_activity_df:69 - Mean values of the rows in the DF is [ 0. -0.  0. ... -0.  0. -0.]
2019-11-25 12:00:37.843 | DEBUG    | pals.pathway_analysis:get_plage_activity_df:70 - Variance in the rows of the DF is [0. 0. 0. ... 0. 0. 0.]
2019-11-25 12:00:40.391 | INFO     | pals.pathway_analysis:set_up_resample_plage_p_df:81 - Calculating plage p-values with resampling
2019-11-25 12:00:40.392 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG16758_F/Wild_F
2019-11-25 12:00:40.392 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
..\pals\pathway_analysis.py:315: RuntimeWarning: invalid value encountered in true_divide
  tvalues = (m1 - m2) / se_total
2019-11-25 12:00:40.494 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:40.587 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:40.681 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:40.775 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:40.872 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:40.966 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:41.064 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:41.159 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:41.260 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:41.353 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 0
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py:901: RuntimeWarning: invalid value encountered in less
  return (a < x) & (x < b)
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py:1892: RuntimeWarning: invalid value encountered in less_equal
  cond2 = cond0 & (x <= _a)
2019-11-25 12:00:41.487 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG16758_M/Wild_M
2019-11-25 12:00:41.488 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:41.583 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:41.678 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:41.777 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:41.871 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:41.973 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:42.087 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:42.198 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:42.297 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:42.392 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:42.489 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 1
2019-11-25 12:00:42.611 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG18128_F/Wild_F
2019-11-25 12:00:42.612 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:42.712 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:42.809 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:42.905 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:43.003 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:43.096 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:43.194 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:43.305 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:43.415 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:43.524 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:43.623 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 1
2019-11-25 12:00:43.734 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG18128_M/Wild_M
2019-11-25 12:00:43.735 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:43.836 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:43.931 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:44.030 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:44.124 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:44.220 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:44.313 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:44.412 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:44.507 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:44.604 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:44.700 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 0
2019-11-25 12:00:44.825 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG1721_F/Wild_F
2019-11-25 12:00:44.826 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:44.921 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:45.015 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:45.107 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:45.207 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:45.301 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:45.403 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:45.497 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:45.593 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:45.687 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:45.786 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 0
2019-11-25 12:00:45.943 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG1721_M/Wild_M
2019-11-25 12:00:45.944 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:46.047 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:46.147 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:46.250 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:46.357 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:46.471 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:46.582 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:46.691 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:46.786 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:46.882 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:46.981 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 1
2019-11-25 12:00:47.122 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG7059_F/Wild_F
2019-11-25 12:00:47.122 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:47.225 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:47.317 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:47.414 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:47.513 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:47.612 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:47.706 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:47.814 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:47.926 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:48.034 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:48.133 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 1
2019-11-25 12:00:48.242 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG7059_M/Wild_M
2019-11-25 12:00:48.243 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:48.340 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:48.438 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:48.532 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:49.888 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:49.992 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:50.087 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:50.190 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:50.293 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:50.391 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:50.490 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 2
2019-11-25 12:00:50.597 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG5345_F/Wild_F
2019-11-25 12:00:50.598 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:50.692 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:50.786 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:50.881 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:50.988 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:51.098 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:51.205 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:51.304 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:51.403 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:51.496 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:51.596 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 0
2019-11-25 12:00:51.719 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG5345_M/Wild_M
2019-11-25 12:00:51.719 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:51.823 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:51.918 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:52.013 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:52.113 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:52.225 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:52.332 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:52.439 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:52.539 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:52.648 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:52.753 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 1
2019-11-25 12:00:52.885 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG6950_F/Wild_F
2019-11-25 12:00:52.886 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
..\pals\pathway_analysis.py:315: RuntimeWarning: divide by zero encountered in true_divide
  tvalues = (m1 - m2) / se_total
2019-11-25 12:00:52.989 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:53.091 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:53.193 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:53.289 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:53.392 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:53.492 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:53.589 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:53.690 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:53.793 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:53.897 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 1
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py:403: RuntimeWarning: invalid value encountered in subtract
  m2 = ((data - mu)**2).mean()
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py:404: RuntimeWarning: invalid value encountered in subtract
  m3 = ((data - mu)**3).mean()
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\numpy\core\_methods.py:193: RuntimeWarning: invalid value encountered in subtract
  x = asanyarray(arr - arrmean)
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\optimize\optimize.py:596: RuntimeWarning: invalid value encountered in subtract
  if (numpy.max(numpy.ravel(numpy.abs(sim[1:] - sim[0]))) <= xatol and
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\optimize\optimize.py:601: RuntimeWarning: invalid value encountered in subtract
  xr = (1 + rho) * xbar - rho * sim[-1]
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py:897: RuntimeWarning: invalid value encountered in less_equal
  return (a <= x) & (x <= b)
c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\optimize\optimize.py:606: RuntimeWarning: invalid value encountered in subtract
  xe = (1 + rho * chi) * xbar - rho * chi * sim[-1]
2019-11-25 12:00:54.160 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:85 - Comparison CG6950_M/Wild_M
2019-11-25 12:00:54.160 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 0/1000
2019-11-25 12:00:54.266 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 100/1000
2019-11-25 12:00:54.375 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 200/1000
2019-11-25 12:00:54.481 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 300/1000
2019-11-25 12:00:54.589 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 400/1000
2019-11-25 12:00:54.700 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 500/1000
2019-11-25 12:00:54.807 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 600/1000
2019-11-25 12:00:54.907 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 700/1000
2019-11-25 12:00:55.006 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 800/1000
2019-11-25 12:00:55.100 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:93 - Resampling 900/1000
2019-11-25 12:00:55.199 | DEBUG    | pals.pathway_analysis:set_up_resample_plage_p_df:99 - Total time 1
2019-11-25 12:00:55.332 | INFO     | pals.pathway_analysis:_calculate_coverage_df:335 - Calculating dataset formula coverage
2019-11-25 12:00:55.335 | INFO     | pals.pathway_analysis:calculate_hg_values:160 - Calculating the hyper-geometric p-values

I added a notebook that reproduces this issue: https://github.com/glasgowcompbio/PALS/blob/master/notebooks/PALS_flymet_analysis.ipynb

joewandy commented 4 years ago

Suspicious warning continues ..

RuntimeWarning                            Traceback (most recent call last)
<ipython-input-18-902c59b1dee3> in <module>
      1 pals = PALS(ds, min_replace=5000)
----> 2 pathway_df = pals.get_pathway_df()

~\Work\git\PALS\pals\pathway_analysis.py in get_pathway_df(self, resample, standardize)
     48         activity_df = self.get_plage_activity_df(standardize)
     49         if resample:
---> 50             plage_df = self.set_up_resample_plage_p_df(activity_df)
     51         else:
     52             plage_df = self.set_up_plage_p_df(activity_df)

~\Work\git\PALS\pals\pathway_analysis.py in set_up_resample_plage_p_df(self, activity_df)
     99             logger.debug('Total time %d' % (stop - start))
    100             tvalues = self._calculate_t_values(activity_df, comparison_samples[0], comparison_samples[1])
--> 101             pvalues = self._compare_resamples(tvalues, null_max_tvalues, null_min_tvalues)
    102             all_pvalues.append(pvalues)
    103 

~\Work\git\PALS\pals\pathway_analysis.py in _compare_resamples(self, tvalues, null_max_tvalues, null_min_tvalues)
    322         minparams = genextreme.fit([-x for x in null_min_tvalues])
    323         for tvalue in tvalues:
--> 324             pvalue = genextreme.sf(tvalue, *maxparams) if tvalue >= 0 else genextreme.sf(-tvalue, *minparams)
    325             pvalues.append(pvalue)
    326         return pvalues

c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py in sf(self, x, *args, **kwds)
   1889         x = np.asarray((x - loc)/scale, dtype=dtyp)
   1890         cond0 = self._argcheck(*args) & (scale > 0)
-> 1891         cond1 = self._open_support_mask(x, *args) & (scale > 0)
   1892         cond2 = cond0 & (x <= _a)
   1893         cond = cond0 & cond1

c:\users\joewa\.virtualenvs\pals-4ls44jcw\lib\site-packages\scipy\stats\_distn_infrastructure.py in _open_support_mask(self, x, *args)
    899     def _open_support_mask(self, x, *args):
    900         a, b = self._get_support(*args)
--> 901         return (a < x) & (x < b)
    902 
    903     def _rvs(self, *args):

RuntimeWarning: invalid value encountered in less