Figure 4: Example diagnostic plots for detecting batch effects and plate-layout effects.

(a) Process of detecting batch effects. The largest matrix on the right shows how plates 1 and 2 are more correlated to each other than to plates 3 and 4, and vice versa. This pattern suggests that plates 1 and 2, as well as 3 and 4, were prepared in batches that have noticeable differences in their experimental conditions. (b) Two plate layouts illustrating the cell count in each well. The visualization allows for identification of plate-layout effects, such as unfavorable edge conditions. Plate 1 shows that cells can grow normally in any well, whereas plate 2 shows markedly lower cell counts at the edges, thus indicating the presence of experimental artifacts.