The correlation coefficient alone is not sufficient to assess equality among sample replicates

Reliability and reproducibility are key metrics for gene expression assays. This report assesses the utility of the correlation coefficient in the analysis of reproducibility and reliability of gene expression data.

The correlation coefficient alone is not sufficient to assess equality among sample replicates but when coupled with slope and scatter plots expression data equality can be better assessed. Narrow-intervals of scatter plots should be shown as a tool to inspect the actual level of noise within the data. Here a team led by researchers at the University of Copenhagen have developed a method to examine expression data reproducibility, which is based on the ratios of both the means and the standard deviations for the inter-treatment expression ratios of genes. In addition, they introduce a fold-change threshold with an inter-replicate occurrence likelihood lower than 5% to perform analysis even when reproducibility is not acceptable. There is no possibility to find a perfect correlation between transcript and protein levels even when there is not any post-transcriptional regulatory mechanism. The researchers therefore propose an adjustment for protein abundance with that of transcript abundance based on open reading frame length.

rna-seq

Availability – This Excel file can be used as an easy tool in order to get the reproducibility measurements. Format: XLTX Size: 3.9MB Download file

Darbani B, Stewart CN. (2014) Reproducibility and reliability assays of the gene expression-measurements. J of Biol Res 21:3. [article]

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