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By Tuimala J., Laine M.M.

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These values are not directly user-definable, but are derived from two user-adjustable parameters, γ 1L and γ 1H, which define the lower and upper boundaries for gamma1. Gamma 2 is computed as a linear interpolation of γ 2L and γ 2H. It is possible to compensate for effects that influence calls based on low and high signals by adjusting the stringency of calls associated with low and high signal ranges (γ L and γ H) independently. This option is not used by default, since gamma values are set as γ 1L = γ 1H and γ 2L = γ 2H.

Natl. Acad. Sci. U S A 97, 12164-9. This chapter was written by Janna Saarela. 34 4 DNA microarray data analysis Overview of data analysis In this book, we emphasize to microarray data analysis after the microarrays have been hybridized, scanned and the images have been analyzed with an image analysis software. Before any experiments in the laboratory have been initiated, the experiment and its analysis should be planned carefully. Chapter 5 describes points that need to be considered when designing the experiments.

T-distribution differs from the normal distribution, because it has an additional parameter, degrees of freedom (df), which affects its shape. Degrees of freedom reflect the sample size. Degrees of freedom can take on any real number greater than zero. A tdistribution with a smaller df has more area in the tails than the distribution with a larger df. As the df increases, the t distribution approaches the standard normal distribution. 4). 5: A typical histogram of the DNA microarray intensity values of one channel (gmean).

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