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The result will be displayed in a child spreadsheet, ANOVA-3way (ANOVAResults). In the child result spreadsheet, each row represents a gene, and the columns represent the computation results for that gene (Figure 4). By default, the genes are sorted in ascending order by the p-value of the first categorical factor. In this tutorial,Type is the first categorical factor, which means the most highly significant differently expressed gene between Down syndrome and normal samples is at the top of the spreadsheet in row 1.

Viewing the Sources of Variation

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Generate these plots for rows 3 (DSCR3) and 8 (CSTB). If the lines in this plot are not parallel, then there is a chance there is an interaction between Tissue and Type. DSCR3 is a good example of this (Figure 7). We can look at the p-values in column 9, p-value(Type * Tissue) to check if this apparent interaction is statistically significant. 

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 The list can be saved as a text file (File > Save As Text File) for use in reports or by downstream analysis software.