A Method for Estimating Limits of Differentially Expressed Levels in cDNA Microarray

Microarrays have become an important technology for the global analysis of gene expression in organisms. For discovery of differentially expressed genes, many cDNA microarray experiments gave a fixed threshold based on a fold change of signal intensity in relative expression level and/or a P value, the deviation of the fixed threshold could be observed by microarray experiments of self-versus-self hybridization. In order to accurately identify differentially expressed genes in two-channel microarray, control experiments through the self-versus-self hybridizations were performed with wheat cDNA microarrays in this study, distribution of extremes of expression levels was obtained from data analysis of the control experiments, and a threshold level was assigned based on the moment distribution method, the differentially expressed genes can be identified when the changes of expression levels of a gene at different treatments falls outside the threshold. This method could be appropriate to estimate the threshold limits and can be applied for cDNA microarray.