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Abbreviations/symbols: Avg. diff., Average difference.

Abbreviations/symbols: Avg. diff., Average difference.

rejected by this test. That is why it is advisable to run replicate experiments using the exact same sample when possible.

Scoring Candidate Probe Sets

Applying the above described test identified about 300 genes worthy of further examination. Which should be examined first? A quick way to decide is to score the candidate probe sets that passed the t test according to their fold change in expression weighted toward higher overall expression values. The mean value of the probe set within each experiment group is used from here on as its expression value within that group.

Score = —- if B is greater than or equal to A, or

The value of variable x is set equal to the expression level deemed significant by the researcher. The list of candidates is then ordered according to this score. Probe sets near the top of the list are overexpressed in group B compared with group A; probe sets near the bottom of the list are underexpressed in group B compared with group A. Although the t value alone can be used to order the data in a similar fashion, the score calculated with this method is similar to the fold change value for the expression range of interest. Thus, the topmost and bottommost entries in this sorted list provide a convenient starting point for evaluation and further experimentation when examined by the critical eye of the researcher.

Acknowledgments

Supported by NIH GM 27345, the Surgery Wound Healing Research Program, and U.S. Surgical, Tyco Healthcare Group. The Laboratory of Molecular Medicine is the research wing of the Center for Minimally Invasive Surgery.

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