Influence of batch effect correction methods on drug induced differential gene expression profiles.

An increasing trend was observed for the methods that correct for two to four PCs.

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These scenarios include different number of batches, allocation ratios and batch effect sizes (see Methods). Generally speaking, with more PCs added to the model, more significant genes were found regardless of the simulation setting applied (Additional file 7 : Figure S7, Additional file 8 : Figure S8, Additional file 9 : Figure S9, Additional file 10 : Figure S10 and Additional file 11 : Figure S11A), although a few cases (vorinostat is especially exceptional across all the simulation settings) demonstrated first an increase, then a decreasing trend when considering different numbers of PCs with PC2 or PC3 as the turning point.

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