Principle Components Analysis of Copy Number Data. Principle Components Analysis PCA is a method of dimensionality reduction to look for overall trends in the data. In figure 1a it can be seen that "scan date" has had a significant impact on the data implying that processing of the samples at different times has contributed significantly to the variance in the samples meaning that this significant contribution may obscure the main effects. Figure 2b shows the PCA plot following batch removal of the effect of Scan Date. A mixed model ANOVA was used to estimate the effect of scan date and removed from the data.