DRAFT
So far we have not looked at any settings. When using ANOVA or creating the report, you may tune the analysis or output
from gdsctools import *
gdsc = ANOVA(ic50_test)
WARNING: column named 'MEDIA_FACTOR' not found TISSUE FACTOR : included MEDIA FACTOR : NOT included MSI FACTOR : included FEATURE FACTOR : included
Everything happens in the settings attribute:
gdsc.settings
{'FDR_threshold': 25, 'MSI_factor_threshold': 2, 'analysis_type': 'PANCAN', 'directory': 'html_gdsc_anova', 'effect_threshold': 0, 'equal_var_ttest': True, 'feature_factor_threshold': 3, 'fontsize': 25, 'include_MSI_factor': True, 'include_media_factor': False, 'low_memory': True, 'minimum_nonna_ic50': 6, 'pvalue_correction_level': 'global', 'pvalue_correction_method': 'fdr', 'pvalue_threshold': inf, 'regression_L1_wt': 0, 'regression_alpha': 0, 'regression_method': 'OLS', 'savefig': False, 'version': '0.10.1', 'volcano_FDR_interpolation': True, 'volcano_additional_FDR_lines': [0.01, 0.1, 10]}
gdsc.settings.analysis_type = 'breast'
gdsc.init()
#results = gdsc.anova_all()
#report = ANOVAReport(gdsc, results)
TISSUE FACTOR : included MEDIA FACTOR : NOT included MSI FACTOR : included FEATURE FACTOR : included
All information can be found in the online documentation but the most important ones are