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To setup ANOVA model, select factors from sample attribute. The factors can be categorical or numeric attribute. Click on a check button to select and click Add factors button to add it to the model (Figure 14).
Figure 14.
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When more than one factors are selected, Add interaction button will be enabled to allow you to specify interaction.
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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).Figure 15:
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Once the model is set, click on Next button to setup comparisons (Figure 16).
Figure 16:
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From the Factor drop-down list to choose a factor or interaction, the subgroup of the factor or interaction will be displayed on the left panel, click to select a subgroup name and move it to one of the right panels, the fold change calculation on the comparison will use the group on the top panel as numerator, and group on the bottom panel as denominator. Click on Add comparison button to add one comparison to the comparisons table. Multiple comparisons can be added to the specified model.
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Click on the Configure to customize Advanced options (Figure 17)Figure 17:
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Low-expression feature and Multiple test correction sections are the same as the GSA advanced option, see above GSA advanced options
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This option is only available when Cufflinks quantification node is selected. Detailed implementation information can be found from Cuffdiff manual [6].
When the task is selected, the dialog will display all the categorical attributes which have more than one subgroups (Figure 18).
Figure 18: Cuffdiff dialog
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