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Chapter 14 Statistical Hypothesis Testing and Differential Expression Analysis A brief description of the various statistical tests in GeneSpring GX appears below. See [26] for a simple introduction to these tests. 14.1 Details of Statistical Tests in GeneSpring GX 14.1.1 The Unpaired t-Test for Two Groups The standard test that is performed in such situations is the so called t-test, which measures the following t-statistic for each gene g (see, e.g., [26]): 2 tg = smm1 −m −m 1 2 r (n −1)s2 +(n −1)s2 1 2 1 2 ( n11 + n12 ) is the unbiased pooled variwhere sm1 −m2 = n1 +n2 −2 ance estimate. Here, m1 , m2 are the mean expression values for gene g within groups 1 and 2, respectively, s1 , s2 are the corresponding standard deviations, and n1 , n2 are the number of experiments in the two groups. Qualitatively, this t-statistic has a high absolute value for a gene if the means within the two sets of replicates are very different and if each set of replicates has small standard deviation. Thus, the higher the t-statistic is in absolute value, the greater the confidence with which this gene can be declared as being differentially expressed. Note that this is a more sophisticated measure than the commonly used fold-change measure (which would just be m1 −m2 on the 451
