Related Experiment Video
Updated: Jul 17, 2026

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
Published on: September 18, 2021
Empirical comparison of tests for differential expression on simulated time series microarray experiments
Ernest A Fischer1, Michael Friedman, Mia K Markey
1Department of Biomedical Engineering,The University of Texas at Austin, Austin, TX, USA.
Abstract:
Methods for identifying differential expression were compared on time series microarray data from artificial gene networks. Identifying differential expression was dependent on normalization and whether the background was removed. Loess after background correction improved results for most methods. On data without background correction median centering improved performance. We recommend Cui and Churchill's ANOVA variants on background subtracted data and Efron and Tibshirani's Empirical Bayes Wilcoxon Rank Sum test when the background cannot be removed.
Related Concept Videos
DNA Microarrays
Multiple Comparison Tests
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...
Comparing the Survival Analysis of Two or More Groups
Comparing Experimental Results: Student's t-Test

