MZquant does not always use data from manual trimming and the final output file has wrong R²-values
Hello Tobias, MZquant does not always use the assigned calibration points after manual trimming. In these cases the file "quantification_table_trimmed_final" still shows the values of the calibration points which I excluded. In the columns "min_sample_neighbor_pos" and "max_sample_neighbor_pos" are the right numbers of the selected calibration points but the values are not deleted and thus also displayed in the graphs in the pdf "quantification_final_gam_plots" and probably they are also used to calculate the calibration functions. When I use the first calibration point: "min_sample_neighbor_pos" = 3 the manual trimming works with every "max_sample_neighbor_pos". However when my "min_sample_neighbor_pos" = 4 or 5 it still uses the calibration point 3 or 3 and 4. A similar problem occurs when I selected "max_sample_neighbor_pos" = 12 and it still uses the point 13. Only when I delete the values for every calibration point I don't want to use it works.
MZquant also writes the old R²-values before the manual trimming to the final output file and notes like "not trimmed" although I did the trimming and set "manual_trim" to "0". The correct R² values are only available in the pdf "quantification_final_gam_plots" but these are also not reliable because it often shows more calibration points than selected.
I hope it's okay to ask you for help and thank you in advance.
Best regards, Paul