Indirect labeling of microarray targets with either Cy3 or Cy5 dyes introduced insignificant levels of noise to microarray data. (a) MA plot for averaged microarray data obtained in two dye-swapped, same vs same target hybridizations. An MA plot plots log-ratio R vs G against the overall intensity of each spot (see text for explanation). The log-ratio is represented by the M value, M = log2(R) - log2(G), and the overall intensity by the A value, A = (log2(R) + log2(G))/2. Targets were obtained by three rounds of T7-amplification (IVTIII). Amean and Mmean were calculated as the averages of M or A values for two microarray experiments and plotted. (b) A volcano plot shows the likelihood of expression difference (LOD) for genes in these two hybridizations selected by an empirical Bayesian method (see Materials and methods for details). The volcano plot shows the relationship between the log2-fold change in expression levels and the LOD to assess the significance of the differences between two targets. There are no genes with LOD greater than zero and thus there are no significant differences between Cy3- and Cy5-labeled targets.
Subkhankulova and Livesey Genome Biology 2006 7:R18 doi:10.1186/gb-2006-7-3-r18