Figure 6.

MAS5 present/absent calls for alternative methods. (a) The average frequency of P values of probesets with present target transcripts generated by the MAS 5.0 present/absent algorithm when using raw PM and MM values (gray), GC-RMA transformed PM and MM values (black) and GC-RMA PM threshold values (blue) are shown. (b) The average frequency of P values of probesets with absent target transcripts (that is, empty probesets) generated by the MAS 5.0 present/absent algorithm.