Mercurial > repos > goeckslab > cell_intensity_processing

diff process_intensities.xml @ 5:afa3cb2110eb draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
author goeckslab
date Thu, 11 Jul 2024 22:41:26 +0000
parents 5d541df02496
children
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--- a/process_intensities.xml	Fri May 10 21:01:41 2024 +0000
+++ b/process_intensities.xml	Thu Jul 11 22:41:26 2024 +0000
@@ -27,7 +27,7 @@
 markers_to_normalize = marker_df['marker_name'].to_list()
 
 #if $AF_method.select_method == 'SBR':
-AF_markers = [x for x in list(marker_df['${AF_method.AF_col}'].unique()) if x != 'None']
+AF_markers = [x for x in list(marker_df['${AF_method.AF_col}'].unique()) if x not in ['None',np.nan]]
 print(f'Detected {quant[AF_markers].eq(0.0).any(axis=1).sum()} cells with AF values of zero in the dataset')
 
 #if $AF_method.AF_filter == 'filter':