Effects of probe set algorithms on absolute expression values and variance. Shown is the same 54 microarray data set from a muscle regeneration 27 time point temporal series , analyzed by five different probe set algorithms. While all probe set algorithms show the same transcriptional induction of this transcript at the day 3.0 time point (expression pattern), the absolute expression levels both at baseline (time 0), and peak expression (day 3.0) computed by the probe set algorithms vary significantly. For example, at baseline, MAS5, dCHIP Difference model, and PCA all show expression near background levels (0), while dCHIP perfect match and RMA show baseline values at 5,000–10,000 units. All graphs are output of the PEPR public access tool .