Duplicated column names in BayesianFoldChangeAnalysis.tsv

[MKoesters]

Hi all,

I used MetaMorpheus to analyse some data and after putting the results into FlashLFQ, I end up with a bayesianFoldChangeAnalysis File with duplicated columns names:

My metamorpheus tomls are these ones here: https://github.com/smith-chem-wisc/MetaMorpheus/issues/2082

['Protein Group',
 'Gene',
 'Organism',
 'Control Condition',
 'Treatment Condition',
 'Null Hypothesis Width',
 'Protein Log2 Fold-Change',
 'Uncertainty in Protein Log2 Fold-Change',
 'Standard Deviation of Peptide Log2 Fold-Changes',
 'Protein Intensity in Control Condition',
 'Protein Intensity in Treatment Condition',
 'Number of Peptides',
 'Number of Control Condition Measurements',
 'Number of Treatment Condition Measurements',
 'Control Measurements',
 'Treatment Measurements',
 'Bayes Factor',
 'Posterior Error Probability',
 'False Discovery Rate',
 'Unnamed: 19',
 'Protein Group.1',
 'Gene.1',
 'Organism.1',
 'Control Condition.1',
 'Treatment Condition.1',
 'Null Hypothesis Width.1',
 'Protein Log2 Fold-Change.1',
 'Uncertainty in Protein Log2 Fold-Change.1',
 'Standard Deviation of Peptide Log2 Fold-Changes.1',
 'Protein Intensity in Control Condition.1',
 'Protein Intensity in Treatment Condition.1',
 'Number of Peptides.1',
 'Number of Control Condition Measurements.1',
 'Number of Treatment Condition Measurements.1',
 'Control Measurements.1',
 'Treatment Measurements.1',
 'Bayes Factor.1',
 'Posterior Error Probability.1',
 'False Discovery Rate.1',
 'Unnamed: 39',
 'Unnamed: 40']

I run FlashLFQ with all standard parameter except specifying --bay and --ctr And then read the data as following:

bay = pd.read_csv(results_dir / "BayesianFoldChangeAnalysis.tsv", sep="\t")

After checking 'Protein Log2 Fold-Change' and 'Protein Log2 Fold-Change.1' I realized the values are not the same, which is bothering me since I don't know if I can continue and if yes, which columns is the right one.

Best, Manuel