Violin plots of Pearson correlation coefficients based on expression profiles after batch correction for comparisons indicated at the x axis. D5, F7 and M8 samples were used to calculate pairwise correlations, whereas D6 samples were used as denominators for calculating ratio-based expressions for correcting batch effects. The number of combinations ( n ) used to derive statistics in c f in each box were as follows: c : intra-batch, n =21; cross-time, n =7; cross-laboratory, n =62; cross-platform, n =43; cross-protocol, n =98; d : intra-batch, n =63; cross-time, n =21; cross-laboratory, n= 186; cross-platform, n =129; cross-protocol, n =294; e and f : intra-batch intra-sample, n =189; intra-batch cross-sample, n =567; cross-time intra-sample, n =189; cross-time cross-sample, n =378; cross-laboratory intra-sample, n =1,674; cross-laboratory cross-sample, n =3,348; cross-protocol intra-sample, n =1,161; cross-protocol cross-sample, n =2,322; cross-platform intra-sample, n =2,646; cross-platform cross-sample, n =5,292.
