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Figure 6 | BMC Bioinformatics

Figure 6

From: BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets

Figure 6

A comparison of down-regulated genes detected after BABAR , scale and quantile normalisation. A Venn diagram showing the relations between down-regulated genes detected by the QGEE software (p ≤ 0.01) for the IHF dataset [22] (WT versus ihfAB double mutant) following either BABAR, limma scale or limma quantile normalisation. For the BABAR processing, the QGEE software analyses were run after background correction with 'within arrays' block-by-block centering of the medians, 'between arrays' cyclic loess with averaging of the log2-ratios, and final centering of the data. For the two limma-implemented normalisation methods the QGEE software analyses were run after the data were background corrected (normexp) with a 'within arrays' method for data centering (printtiploess), followed by a 'between arrays' method, either quantile or scale normalisation.

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