Figure 4

Batch Summary of Cleansing Process. Batch characteristics resulting from the affy package analysis. Boxplots (top row) and densities (bottom row) of the Bhattacharjee data: summary of batch intensities. The color of batch results is consistent in all graphs, as indicated in the key in the B panels. The y-axes are the log₂ of the intensities of the probes in a batch. Panels A1 and B1 depict the completely unfiltered data set, including all probes and Batch 3: note the obvious offset in Batch 3 and the strong skew to the resulting distributions. Panels A2 and B2 show the effects of removing Batch 3 and additional outlying samples, but include all probes: the skew remains significant but no batches are outliers. Panels A3 and B3 show the output after both sample cleansing and BaFL probe filtering: the distribution is more normal but the tails have been truncated. Note that the total density scale in panel B3 is reduced relative to B1 and B2 because fewer probes are included and less variance is observed. Similar output for the Stearman experiment is provided as Additional file 3[19].