Additional file 1.

Scatterplots comparing methods of normalization and expression summarization. A pair of hybridization replicates, ant 1 E and ant 2 E, were chosen to illustrate differences in data distribution after processing with different methods to produce a final expression measure for each gene. All values are log₂ transformed and ant 1E gene values are plotted on the y-axis against ant 2 E on the x-axis. The red line indicates no difference in expression level between replicates, and the black lines indicate 2-fold changes between the replicates. Larger numbers of points far from the red diagonal indicate less correspondence between the replicates. Results were similar for a separate set of replicates (not shown). (A) RMA; (B) dchip perfect match (PM) only; (C) MAS 5.0; (D) dchip perfect match minus mismatch (PM-MM).

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Skinner and Gasser BMC Plant Biology 2009 9:29   doi:10.1186/1471-2229-9-29