Extended Data Fig. 3: Comparison of Milo and MELD for abundance fold change estimation.
From: Differential abundance testing on single-cell data using k-nearest neighbor graphs
(a–d) Scatter-plots of the true fold change at the neighbourhood index against the fold change estimated by Milo (A,C) and MELD (B,D), without batch effect (a, b) and with batch effect (magnitude = 0.5) (c, d), where LFC = log(pc’/(1 - pc’)). The neighbourhoods overlapping true DA cells (pc’ greater than the 75% quantile of P(C1) in the mouse gastrulation dataset) are highlighted in red. (e, f) Mean Squared Error (MSE) comparison for MELD and Milo for true negative neighbourhood (e) and true positive neighbourhoods (f), with increasing simulated log-Fold Change and magnitude of batch effect. Each boxplot summarises the results for n=27 simulations. Box plots show the median with interquartile ranges (25–75%); whiskers extend to the largest value no further than 1.5x the interquartile range from the distance from the box, with outlier data points shown beyond this range.
