Figure 7.

Dual-target: MA plots before/after normalisation (A) MA plots for each combination of dye-labelled samples in the dual-target arrays. The number of replicated experiments here is smaller (n = 2 arrays for each dye-label combination), but the trends are confirming that the performance of the dye-labels is very similar in the absence of a third dye-label on the array. All dual-target hybridisations involving Cy5 dye have higher levels of error in the log-ratios towards the lower end of the expression spectrum. The combination Cy3/Alexa594 shows none or only small levels of this effect. (B) After LoWeSS and MAD scale normalisation, log-ratios for all dual-target combinations are broadly similar.