Target cDNA from SW480 was labelled with Cy3 whereas cDNA from SW620 was labelled with Cy5 using the amino-allyl labelling method. Both cDNA pools were co-hybridised on glass slides with 8448 spots. The spots consisted of 3986 distinct sequence-verified human cDNA clones (Research Genetics, release GF211) printed in duplicates, 84 spots from non-human cDNA clones and a further 154 control spots. Spots were printed by 4x4 pins. The experiment consisted of four replicated arrays derived from separate labelling reactions. Local background spot intensities were extracted by QuantArray software (version2.1). Analysis showed that replicated spots were highly correlated (average Pearson correlation: 0.94). Since this may interfere with the efficiency testing performed (and to reduce the size of the data set for illustration purpose), the replicated spots were not included here. Experimental details and further analysis can be found in Futschik et al. (2002).
data(sw)sw.olin