Short CommunicationIdentification of differentially expressed genes using multi-resolution wavelet transformation analysis combined with SAM

Although many statistical methods have been proposed for identifying differentially expressed genes, the optimal approach has still not been resolved. Therefore, it is necessary to develop more efficient methods of finding differentially expressed genes while accounting for noise and false discovery rate (FDR). We propose a method based on multi-resolution wavelet transformation analysis combined with SAM for identifying differentially expressed genes by adjusting the Δ and computing the FDR. This method was applied to a microarray expression dataset from adenoma patients and normal subjects. The number of differentially expressed genes gradually reduced with an increasing Δ value, and the FDR was reduced after wavelet transformation. At a given Δ value, the FDR was also reduced before and after wavelet transformation. In conclusion, a greater number and quality of differentially expressed genes were detected using the method when compared to non-transformed data, and the FDRs were notably more controlled and reduced.

► Explore better combinations of WT-SAM methods for identifying differentially genes. ► We have obtained meaningful and valuable results by adjusting the Δ and FDRs. ► A greater number and quality of differentially expressed genes were detected. ► Compared to non-transformed data, the FDRs was notably more controlled and reduced.