A new method for estimating the number of non-differentially expressed genes

Abstract

ABSTRACT. Control of the false discovery rate is a statistical method that is widely used when identifying differentially expressed genes in highthroughput sequencing assays. It is often calculated using an adaptive linear step-up procedure in which the number of non-differentially expressed genes should be estimated accurately. In this paper, we discuss the estimation of this parameter and point out defects in the original estimation method. We also propose a new estimation method and provide the error estimation. We compared the estimation results from the two methods in a simulation study that produced a mean, standard deviation, range, and root mean square error. The results revealed that there was little difference in the mean between the two methods, but the standard deviation, range, and root mean square error obtained using the new method were much smaller than those produced by the original method, which indicates that the new method is more accurate and robust. Furthermore, we used real microarray data to verify the conclusion. Finally we provide a suggestion when analyzing differentially expressed genes using statistical methods.

UGM: a more stable procedure for large-scale multiple testing problems, new solutions to identify oncogene

“…These results suggested that the UGM method and S-λ method are significantly superior to the ABH and the TST methods. In addition, the SD, range, quartile range, CV and RSME of the number of non-differentially expressed genes calculated by the S-λ method were all larger than those of the UGM method and are more discrete, which is concordant with the study by Wu Jing [16]. In summary, the UGM exhibited better stability, accuracy and robustness,which was better than other conventional algorithms.…”

“…The results displayed that the UGM method was significantly more powerful than the general t-test ( p = 0), and has slightly larger set of differentially expressed genes than those of the ALSU, presenting lower false negative rate and higher screening efficiency. In the differentially expressed genes screened by UGM method, a bunch of well-established oncogenes and anti-oncogenes were discovered, including BRCA1, BRCA2, PTEN, BRIP1 [20], RAD51 [21], BARD1 [16, 17], MMP11 [22], RRM2 [23], NEK2 [24] et al Furthermore, genes associated with BRCA1, BRCA2 and TP53 were also identified, such as ITGA7 [25], CXCL5 [26] etc.…”

“…For type I error, the FDR controlling procedure is not as strict as family wise error rate (FWER) controlling procedures, which controls the probability of more than one type I error [15]. Therefore, FDR controlling programs have an advantage over type I errors, but at the cost of increasing the error rate [16, 17]. At the same time, the results of different methods are quite different.…”