gene level thresholding code questions

[hmbaghdassarian]

Hi there,

A couple questions regarding the GeneLevelThresholding class:

1. The assignment of the global_quantiles attribute in the __init__ method (line 56) currently takes the mean across the local quantiles. These values are different then if you were to flatten the whole matrix and take the quantiles like that (pd.Series(omics_dataframe.values.flatten()).quantile(qvalues)). Is this correct, or should it be taking the quantiles across the flattened values?
2. The call to local_t2_thresholding (line 176) assigns gtup as self.global_threshold_lower. Should this be assigned up self.global_threshold_upper instead? If not, is self.global_threshold_upper not being used?

Thanks!