Figure 7

Distributions of t-statistics calculated from different expression measures for genes that are completely absent in the Breast Cancer data. The same default normalization procedures as in Figure 2 were applied. The t-statistics compare expression values between users and non-users of hormone replacement therapy (HRT) in the sample as in Figure 4. The density curves show the smoothed histograms of the test statistics for 4371 probe sets that had absent calls on all 159 chips. The MAS5 curve is centered at zero and close to a standard normal distribution expected approximately if no gene is differentially expressed between HRT users and non-users. The RMA curve is strongly shifted to the left, indicating wide-spread down-regulation of numerous absent genes in non-users; the MBEI curve shows moderate asymmetry and heavy tails at both sides, indicating more moderate, but still common gene regulation. Given the low signal quality of these genes that were classified as absent throughout the data set, small or no detectable regulation effects seem biologically most plausible.