Reproducibility of gene expression across generations of Affymetrix microarrays

BMC Bioinformatics

Table 1 The correlation coefficient for pair wise comparisons of samples within and across chip generations and scanner settings.

	No. of probe sets U95A / Low Gain in common		U95A / Low Gain	Correlation (r)
Experiment				MAS 4.0	MAS 5.0
1	12,625	Chip3	Chip4	0.994	0.993
		Chip7	Chip8	0.996	0.989
		U95A / High Gain	U95A / Low Gain
2	12,626	Chip2	Chip3	0.847	0.846
		Chip6	Chip7	0.756	0.753
	12,600	Chip10	Chip11	0.843	0.815
		Chip13	Chip14	0.824	0.827
		HuGeneFL/High Gain	HuGeneFL/Low Gain
3	7,129	Chip15	Chip16	0.906	0.912
		Chip18	Chip19	0.904	0.913
		Chip21	Chip22	0.947	0.955
		HuGeneFL/High Gain	U95A / Low Gain
4	8,044	Chip1	Chip4	0.745	0.802
		Chip5	Chip7	0.730	0.719
		Chip9	Chip11	0.749	0.690
		Chip12	Chip14	0.798	0.760
		Chip15	Chip17	0.818	0.792
		Chip18	Chip20	0.803	0.766
		Chip21	Chip23	0.810	0.789

ISSN: 1471-2105