Strand specificity of in situ produced sense/antisense cDNA microarray features. (a) Histogram showing the distribution of log2 ratios after hybridization to single stranded C (blue), N (red), and double stranded CN (gray) capture probes with labelled Cy3- M13 forward and Cy5 – reverse sequencing primers (The log2 ratios for C and N probes from cDNA clones of plate IRAT3 were centered around -5 and 5 respectively, as expected since their cloning sites were reversed compared to the other clones, but to simplify the presentation the values are inverted). (b) log2 ratios for probes shown in panel matched on cDNA clone ID and sorted on ascending log2 ratio for the respective CN probe. (c) Mean log2ratios for β-lactamase spike-in sense (blue) and antisense (red) control features for hybridizations A to I. For individual features, log2 ratios were calculated using untransformed background corrected data (Median FG – Median BG). For mean log2 ratio calculations, only features where MedianFG > MedianBG in both channels, i.e. Cy3 and Cy5, and where SNR > = 3 in either channel, were included. Error bars denote +/-1SD. Mean log2ratio were calculated using values from between 66 and 70 replicated control spots.