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. 2013 Jul 2;8(7):e67019. doi: 10.1371/journal.pone.0067019

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© 2013 Fernandes et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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A comparison of within-condition gene expression-difference to the median expression level for three different experiments. The left panel shows the sampling variance for comparison and the three experiments are shown in subsequent panels. The L-K RNA-Seq data set compares gene expression in two liver and two kidney samples. The Bacillus cereus RNA-Seq data set for samples grown at neutral pH and two samples 20 minutes after shift to grown at low pH. Meta-RNA-Seq data is for microbial gene expression analysis of four clinical vaginal samples from two women with a healthy microbiota and two women with a microbiota indicative of bacterial vaginosis. The RNA-Seq experiments in the L-K and B. cereus datasets were from controlled conditions with identical gene content per condition and show that the vast majority of highly-expressed genes have small within-condition estimates of , and that estimate only becomes imprecise as becomes very small. The Meta-RNA-Seq panel shows that when within-condition variance is high, there is no relationship between the expression level and the within-condition variance. Note that base-2 logarithms were used throughout.

Inline graphic — A comparison of within-condition gene expression-difference to the median expression level for three different experiments. The left panel shows the sampling variance for comparison and the three experiments are shown in subsequent panels. The L-K RNA-Seq data set compares gene expression in two liver and two kidney samples. The Bacillus cereus RNA-Seq data set for samples grown at neutral pH and two samples 20 minutes after shift to grown at low pH. Meta-RNA-Seq data is for microbial gene expression analysis of four clinical vaginal samples from two women with a healthy microbiota and two women with a microbiota indicative of bacterial vaginosis. The RNA-Seq experiments in the L-K and B. cereus datasets were from controlled conditions with identical gene content per condition and show that the vast majority of highly-expressed genes have small within-condition estimates of , and that estimate only becomes imprecise as becomes very small. The Meta-RNA-Seq panel shows that when within-condition variance is high, there is no relationship between the expression level and the within-condition variance. Note that base-2 logarithms were used throughout.