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When more than one factor is added to the model, click on the Cross tabulation link at the bottom to view the relationship between the factors (Figure 15).

Once the model is set, click on Next button to setup comparisons (contrasts) (Figure 16).

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When the task is selected, the dialog will display all the categorical attributes more than one subgroups (Figure 18).

When an attribute is selected, pairwise comparisons of all the levels will be performed independently.

Click on Configure button in the Advanced options to configure normalization method and library types (Figure 19).

There are three library normalization methods:

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The report of the cuffdiff task is a table of a feature list p-values, q-value and log2 fold-change information for all the comparisons (Figure 20).

In the p-value column, besides an actual p-value, which means the test was performed successfully, there is also the following flags which indicate the test was not successful:

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