There was good correlation between Y-27632–treated cells and matched controls, with
R 2 = 0.977 ± 0.004 (mean ± SD,
n = 3) for U95A chips and
R 2 = 0.976 ± 0.004 (mean ± SD,
n = 6) for U133A chips. These data highlight the relatively small effect of Y-27632 and the excellent chip-to-chip reproducibility when similar samples are analyzed. They are comparable with the
R 2 (0.95) for chip-to-chip reproducibility previously reported,
25 using corneal fibroblasts derived from a single tissue source. Comparisons between samples from different donor corneas which were treated identically in vitro gave regression coefficients of
R 2 = 0.939 ± 0.013 (mean ± SD,
n = 6: U133A chips). Analysis of corneal epithelial cells on U95A chips (Harvey SAK, SundarRaj N, unpublished data; 2002) gave
R 2 = 0.970 ± 0.022 (mean ± SD,
n = 3) for the Y-27632 effect and 0.900 ± 0.044 (mean ± SD,
n = 6) for donor-to-donor variation. Taken together, these data show that donor-to-donor variation is greater than chip-to-chip variation for both chip formats and led us to select candidates on the basis of consistent multiples of change (
x-fold) in pair-wise comparisons rather than requiring consistent absolute changes in expression.