The function calculate_protein_abundance() previously only removed proteins from quantification that had less than 3 peptides in all conditions. Now it removes proteins from quantification (for each sample separately) if they have less than 3 peptides identified in the sample.
The function
calculate_protein_abundance()previously only removed proteins from quantification that had less than 3 peptides in all conditions. Now it removes proteins from quantification (for each sample separately) if they have less than 3 peptides identified in the sample.