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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.

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