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In this tutorial, the overall p-value for the factor (column 4) is the same as the p-value for the linear contrast (column 5) as there are only two levels within Tissue. If we had more than two groups, the overall p-value and the linear contrast p-values would most likely differ. You can also see the ? symbol in the ratio/fold-change columns (6 and 7) for several genes that also have a low p-value because there are zero reads in one of the groups, thus making it impossible to calculate ratios and fold-changes between groups.

For a more detailed example of ANOVA set upusing ANOVA with more complicated experimental designs, including multiple factors and linear contrasts, please refer to Identifying Differentially Expressed Genes using ANOVA in the Gene Expression Analysis tutorial.

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