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Figure 1. Correlation of Brassica genomic and mRNA microarray hybridizations with Arabidopsis genomic DNA and with Brassica replicates. Scatterplots of expression signal values derived from Arabidopsis and Brassica genomic DNA hybridization to the Arabidopsis microarray are shown. Expression metrics for probesets were calculated from the 72nd percentile value of all perfect match probe tiles for each transcript. This was done either including all probes in each probeset (top left) or after excluding "bad" probes that show less than 75% of the hybridization signal to Brassica genomic DNA compared to Arabidopsis genomic DNA (top right). The bottom scatterplots show the reproducibility of replicate hybridizations to Brassica mRNA samples using the standard analysis (bottom left) and excluding "bad" probes (bottom right).
