Additional file 3.
Number of differentially expressed genes identified in replicate analyses. Numbers of genes reported to be differentially expressed after standard analysis (quantile normalisation) (left), after a standard analysis with mean-centring (middle), and after a standard analysis augmented with the ComBat batch correction (right). A and B refer to the results from independent analyses of the duplicate sample groups while C refers to the results from the pooled duplicate samples. The rows of Venn diagrams illustrate the results with (i) limma, (ii) SAM, (iii) limma using UHRR, and (iv) SAM using UHRR.
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Kitchen et al. BMC Genomics 2010 11:134 doi:10.1186/1471-2164-11-134