Illustration of the TMDH microarray scoring system (see text). a) Histogram of log2 of the raw microarray signals. b) As a), but overlaid with histogram of log2 of the microarray signals for the probes which do not hybridise to the S. aureus NCTC 8325 genome sequence, and hence indicate the background signal level in the absence of labelled transcript. c) A normal curve is fitted empirically to the data to model the distribution of background signals. d) Cut-offs are defined to classify the probe signals as reflecting the presence (+1) or absence (-1) of transposons. Probes with an intermediate signal are scored as 0, and effectively omitted from the analysis.