Figure 3

Genes (A) differentially (p < 0.05) or (B) ± 2-fold differentially (p < 0.05) expressed in one or more of the three treatment conditions in Arabidopsis thaliana in which RNA was extracted from whole rosettes of 7, 14, and 21 d old plants, labelled and hybridised to the A. thaliana ATH1-121501 GeneChip array ([24]; n = 3) and normalised to the median expression value of each gene across all time points. Filled circles represent probe-pairs removed from the analysis using gDNA hybridisation intensity thresholds. Open circles represent random removal of 1, 2, 5, 10, 20, 50, 75 and 90% of probe-pairs from an Arabidopsis gDNA .cel files. Random probe removal was repeated on three occasions (error bars represent ± S.E.M). (C) Genes identified as significantly differentially expressed (p < 0.05) in the absence of a probe-mask, as a proportion of the sum of all genes significantly differentially expressed (p < 0.05) when analyses were conducted with and without a corresponding probe-mask. All panels are expressed as a function of the percentage of probe-pairs removed from the analysis either by random simulation, or by gDNA hybridisation.