Previously we have reported a microarray image processing and data analysis package Matarray, where quality scores are defined for every spot that reflect the reliability and variability of the data acquired from each spot. In this article we present a new development in Matarray, where the quality scores are incorporated as weights in the statistical evaluation and data mining of microarray data. With this approach filtering of poor quality data is automatically achieved through the reduction in their weights, thereby eliminating the need to manually flag or remove bad data points, as well as the problem of missing values. More significantly, utilizing a set of control clones spiked in at known input ratios ranging from 1:30 to 30:1, we find that the quality-weighted statistics leads to more accurate gene expression measurements and more sensitive detection of their changes with significantly lower type II error rates. Further, we have applied the quality-weighted clustering to a time-course microarray data set, and find that the new algorithm improves grouping accuracy. In summary, incorporating quantitative quality measure of microarray data as weight in complex data analysis leads to improved reliability and convenience. In addition it provides a practical way to deal with the missing value issue in establishing automatic statistical tests.