Exploratory methods for checking quality of microarray data

In microarray experiments many undesirable systematic variations are commonly observed. Often investigators analyzing microarray data need to make subjective decisions about the quality of the experiment, by examining its chip image and a simple scatter plot. Thus, a more rigorous but simple method is desirable to determine the quality of microarray data. We propose two exploratory methods to investigate the quality of microarray experiments with replicated chips. The first method is based on correlations among chips and the second on the actual intensity values for each gene. The proposed methods are illustrated using a real microarray data set. The methods provide an initial estimation for determining the quality of microarray experiments.