Experimental design for microarray hybridizations. Samples tested positive for either PNRSV, PLMVd, both pathogens simultaneously, or healthy controls were analysed in four independent biological replicates and two technical replicates (dye swaps: Cy3-healthy/Cy5-infected or Cy3-infected/Cy5-healthy). Each biological replicate (numbered 1 to 4) for each infection and healthy plants consisted of a pool of four infected peach fruits from four different trees. The different sets of probes were hybridized to a cDNA microarray representing all the unigenes in the ChillPeach database. In detail, microarray hybridizations were performed by hybridizing each virus infected biological replicate and the healthy control replicate to an array resulting in a total of 16 hybridizations. Dye swaps were performed for two of the four replicates of each infection.