Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics

Background: In genetic transcription research, gene expression is typically reported in a test sample relative to a reference sample. Laboratory assays that measure gene expression levels, from Q-RT-PCR to microarrays to RNA-Seq experiments, will compare two samples to the same genetic sequence of interest. Standard practice is to use the log2-ratio as the measure of relative expression. There are drawbacks to using this measurement, including unstable ratios when the denominator is small. This paper suggests an alternative estimate based on a proportion that is just as simple to calculate, just as intuitive, with the added benefit of greater numerical stability. Results: Analysis of two groups of mice measured with 16 cDNA microarrays found similar results between the previously used methods and our proposed methods. In a study of liver and kidney samples measured with RNASeq, we found that proportion statistics could detect additional differentially expressed genes usually classifie...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Tracy L. Bergemann, Jason Wilson
• Keywords: Biometrics, BMCBI 2011, Distributional Assumptions, Expression Values, Gene Expression Levels