Figure 2.

Cadmium effects on gene expression: Buffers, blanks, and controls. Gene expression data from control and cadmium (20 μg Cd/L for 48-h) treated Daphnia pulex [GEO:GSE9746]. Data were LOESS normalized; duplicate probes were averaged within LIMMA using gene-wise linear models fit to expression data, and gene expression log ratios (M = log2 treated/control) were plotted against log mean intensity values (A = 1/2log2 (treated * control). Print control elements (buffers, blanks, betaine; grey shades); negative controls (non-daphniid cDNA; pink); and positive controls (D. pulex cytochrome b and c, actin, and ferritin; green) are highlighted.

Shaw et al. BMC Genomics 2007 8:477   doi:10.1186/1471-2164-8-477
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