Figure 2.

HiTSeekR produces a series of plots for quality control. (A) Box plots of all plates and replicates. (B) Replicate correlation plot including a linear regression (black line) with corresponding R² correlation factor. The grey line indicates the identity. (C) Signal spread of the various controls across all plates. The positive controls rela and tnfr1 are more robust than the negative controls sicon and lrp5. (D) Control separability measured by SSMD. Here, the separability between the negative control lrp5 and the other controls is shown. The red area indicates bad separability and the orange area good separability. An SSMD outside of the orange area indicates excellent separability. (E) Plate signal is centered by the mean and subsequently column means are plotted across all plates and replicates to indicate positional effects typically evident by a u-shape.