Additional file 8: Figure S6.
The Robust Multi-array Average algorithm minimizes standard deviations in microarray data of mRNA translation state (TL; ribosome occupancy). (A) Averages of translation states (log2 TL) were calculated for four replicates of wild-type reference samples drawn from the pab2 pab8 mutant experiment. (B) Genes were binned according to the standard deviations (SD) of their translation state. All Arabidopsis genes (n = 22,746) represented on the GeneChip® Arabidopsis ATH1 Genome Array were analyzed. Note that the fraction of genes with SD >0.4 is minimized when using RMA. Reference samples (mock treatment) taken from hypoxia  and Turnip Mosaic Virus (TuMV) infection  datasets also showed similar distributions with RMA consistently giving lower variability (SD <0.5) of log2 TL values between replicates (not shown). (C-F) Comparison of the number of differentially translated genes (DTGs) between RMA-normalized and gcRMA-normalized data. Changes in translation state (Δlog2 TL) of RMA-normalized (C,D) and gcRMA-normalized (E,F) data for the rpl24b and eif3h datasets. Values on the x-axes show the fold changes in translation state in the respective mutant over wild-type samples. Y-axes show statistical significance of these changes according to limma/false discovery rate (FDR) adjusted P values, log transformed ('volcano plot’). Horizontal dashed lines mark the FDR <0.05 (-log value = 1.3) cut-off. The vertical dashed lines delineate 1.5-fold changes in upward (red) or downward (blue) directions. All Arabidopsis genes (n = 22,746) represented on GeneChip® Arabidopsis ATH1 Genome Array were analyzed. In (F) the legend explains the color coding used to illustrate different levels of significance.
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Tiruneh et al. BMC Biology 2013 11:123 doi:10.1186/1741-7007-11-123