The effect of normalization on microarray data analysis

This paper contains a description of several common normalization methods used in microarray analysis, and compares the effect of these methods on microarray data. The importance of background subtraction is also addressed. The research focuses on three parts. The first uses three statistical methods: t-test, Wilcoxon signed rank test, and sign test to measure the difference between background subtracted data and nonbackground subtracted data. The second part of the study uses the same three statistical methods to compare whether data normalized with different normalization methods yield similar results. The third part of the study focuses on whether these differently normalized data will influence the result of gene selection (dimension reduction). The comparisons are done for several data sets to help identify similarity patterns. The conclusion of this study is that background subtraction can make a difference, especially for some data sets with poorer quality data. The choice of normalization method, for the most part, makes little difference in the sense that the methods produce similarly normalized data. But, based on the third part of analysis, we found that when gene selection is performed on these differently normalized data, somewhat different gene sets are obtained. Thus, the choice of normalization method will likely have some effect on the final analysis.