Figure 3

Correlations for the Breast Cancer data set normalized using a predefined set of 100 houskeeping genes. The MAS5 expression values were normalized both before and after taking the logarithm, corresponding to MAS5 (raw) and MAS5 (log). The RMA and MBEI expression values were normalized after caculating the logarithmized expression values, see Methods. Top left: The distributions of the correlation coeffcients are not centered at zero. Top right and bottom: Mean correlations versus median product of standard deviations are shown as in Figure 2, comparing the residual correlation for the housekeeping normalization and the default procedure for each expression measure (as indicated in the legends). Housekeeping normalization does much worse than the default in removing the systematic relationships. In case of the MAS5 values, both variants do worse than the default, and the normalization of the raw (un-logged) values doing worse than that of the logarithmized values.