The Reporter Ions Quantifier node and the Precursor Ions Quantifier node calculate the coefficients of variation of the grouped abundances from the abundances of the individual replicates within each group, as follows:
grouped abundances CV = 100 ´ std.dev / median(abundance(replicate_1), …, abundance(replicate_n))
Other CVs are calculated accordingly.
The variability of the pairwise ratios is calculated from the all pairwise ratios of all peptides of a protein, as follows:
variability pairwise ratio = 100 ´ 1.483 MAD(ratio_1, …, ratio_m) / (median_fold_change)
where
- MAD is the median absolute deviation
- median_fold_change is the median_ratio when this is larger or equal to one;
otherwise, median_fold_change is 1/median_ratio
In all cases where medians are taken, we use the geometric median; that is, for an even number of elements, we take the geometric_average of the two elements in the middle.