Figure 4.

MA plots for the Latin square data, generated by affycomp [4]. Points represent probesets targeting transcripts not expected to change, numbers represent probesets targeting transcripts spiked into the dataset at different concentration. The number represents the expected fold change. Fold change is represented by M on the y-axis. A: RMA processed data. B: Raw MAS5 processed data. C: filtered-MAS5 data. Raw MAS5 data suffers from a significant number of False Positives (i.e. probesets recording a differential expression greater than 2-fold), while RMA shows much better performance on these data. Filtering MAS5 data by detection call as described in Methods, significantly reduces the number of False Positives and brings the results much closer to those of RMA.