studies have been published comparing competing platforms with mixed results: some find agreement (Kane et al. 2000; Hughes et al. 2001; Yuen et al. 2002; Barczak et al. 2003; Carter et al. 2003; Wang et al. 2003), others do not (Kuo et al. 2002; Kothapalli et al. 2002; Li et al. 2002; Tan et al. 2003). Why the disagreement? Two possibilities were that 1) different statistical assessments were used and 2) the lab effect was not explored. That different statistical assessments can lead to different conclusions is clear and we will give an example later. To see how the lab effect can result in different conclusions, consider that in all previous studies, platform variation was confounded with technician/lab variation. In the cases where the same lab created all the microarray data it was clear that they had more experience with one of the platforms being compared. The lab effect has been shown to be particularly strong. For example, in a 1972 paper, W.J. Youden (Youden 1972) pointed out how different Physics labs published speeds of light estimates with confidence intervals that made the differences between labs statistically significant (see Figure 2-1). Notice, that if we do not take the lab effect into account this would imply that the speed of light is different in the different labs! It is no surprise that similar effects are present in biology labs and that it does not only apply to microarray measurements.

FIGURE 2-1 Speed of light estimates with confidence intervals (1900-1960). Source: Youden 1972. Reprinted with permission; copyright 1972, Journal Information for Technometrics.

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