From 7589632e2bcf34d102a88e91a58f77a47a05612c Mon Sep 17 00:00:00 2001 From: Boris MUZELLEC Date: Thu, 12 Jan 2023 15:53:28 +0100 Subject: [PATCH 1/2] refactor: remove useless print statement --- pydeseq2/DeseqStats.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pydeseq2/DeseqStats.py b/pydeseq2/DeseqStats.py index cbd59515..cdd5dd37 100644 --- a/pydeseq2/DeseqStats.py +++ b/pydeseq2/DeseqStats.py @@ -185,7 +185,6 @@ def __init__( ) self.LFCs.iloc[:, 0] += self.LFCs.iloc[:, self.contrast_idx] self.LFCs.iloc[:, self.contrast_idx] *= -1 - print(self.LFCs.columns[self.contrast_idx]) # Set a flag to indicate that LFCs are unshrunk self.shrunk_LFCs = False self.n_processes = get_num_processes(n_cpus) From d20b27dc495131f0441af80e8e50d53a234963de Mon Sep 17 00:00:00 2001 From: Boris MUZELLEC Date: Thu, 12 Jan 2023 15:56:32 +0100 Subject: [PATCH 2/2] refactor: remove deprecated _change_lfc_sign attribute --- pydeseq2/DeseqStats.py | 7 ------- 1 file changed, 7 deletions(-) diff --git a/pydeseq2/DeseqStats.py b/pydeseq2/DeseqStats.py index cdd5dd37..d6594bcb 100644 --- a/pydeseq2/DeseqStats.py +++ b/pydeseq2/DeseqStats.py @@ -190,7 +190,6 @@ def __init__( self.n_processes = get_num_processes(n_cpus) self.batch_size = batch_size self.joblib_verbosity = joblib_verbosity - self._change_lfc_sign = False def summary(self): """Run the statistical analysis. @@ -255,12 +254,6 @@ def run_wald_test(self): .values ) - # If the contrast implies a different reference level than the one from the - # design matrix, change lfc signs. Do this *after* the means were computed - # (otherwise we would need) - if self._change_lfc_sign: - self.LFCs.iloc[:, self.contrast_idx] *= -1 - # Set regularization factors. if self.prior_disp_var is not None: ridge_factor = np.diag(1 / self.prior_disp_var**2)