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To specify individual pair wise comparisons, press the Contrast button. Contrasts are performed on groups already defined in the ANOVA model. If two tissue types should be compared to each other, select the tissue term from the Select Factor/Interaction dropdown in the upper left. Select either one or a set of categories and add them to group 1 and group 2. All samples falling into group 1 will be compared to all samples falling into group 2. Output will include not only a p-value, but also a fold change. This fold change will represent the average fold change of the GO category between the two groups. Fold change is calculated as Group 1 divided by Group 2. For data in log space, the data is antilogged as well; fold change output is always for data on a linear scale.

Excluding Genes

Check Exclude probe sets and differential expression p-value(s) > to filter out probe sets (=genes) which are not express in any of the genes. The Exclude probe sets option will remove any gene that meets the specified limit. Using the default options, this will remove low expression genes. Note that the default value of 3 is a suggestion for Affymetrix expression arrays and may not be applicable for other data sets. We suggest to perform exploratory analysis and inspect the distribution of the expression values first (e.g. View > Histogram > Row or View > Box and Whiskers > Row). The sub-checkbox, differential expression p-values, provides an override to the low expression limit. Here, a gene will be included in the analysis despite a low expression value if the gene displays a p-value below the specified limit, suggesting that the gene is differentially expressed