Table 2.

By-Gene medians and median absolute deviation

	Triple-self hybridisations Median (MAD)	Self-self hybridisations Median (MAD)
Cy5 / Cy3	0.024 (0.141)	0.0153 (0.0943)
Cy5 / Alexa594	0.013 (0.170)	0.0066 (0.1609)
Cy3 / Alexa594	-0.001 (0.145)	0.0068 (0.1486)

For each gene on the array, the median and median absolute deviation (MAD) of a particular log-ratio (e.g. Cy5/Cy3) across the 5 arrays * 2 spot replicates per array (effective n = 10) was obtained. The median value of all genes' median log-ratios and all genes' MAD is the basis of the estimate in this table. The effective n for the self-self hybridisations was 2 arrays per dye-label combination * 2 spot replicates per array = 4 measurements.