Background: Quantile and rank normalizations are two widely used pre-processing techniques designed to remove technological noise presented in genomic data. Subsequent statistical analysis such as gene differential expression analysis is usually based on normalized expressions. In this study, we find that these normalization procedures can have a profound impact on differential expression analysis, especially in terms of testing power.
Results: We conduct theoretical derivations to show that the testing power of differential expression analysis based on quantile or rank normalized gene expressions can never reach 100% with fixed sample size no matter how strong the gene differentiation effects are. We perform extensive simulation analyses and find the results corroborate theoretical predictions.
Conclusions: Our finding may explain why genes with well documented strong differentiation are not always detected in microarray analysis. It provides new insights in microarray experimental design and will help practitioners in selecting proper normalization procedures.