Now that the data has been imported, we need to make a few changes to the data annotation before analysis.
Notice that the Sample ID names in column 1 are gray (Figure 1). This indicates that Sample ID is a text factor. Text factors cannot be used as a variable in downstream analysis so we need to change Sample ID to a categorical factor.
Figure 1. Viewing the imported data in a spreadsheet
Right-click on the column header to invoke the pop-up menu
Select Properties (Figure 2)
Figure 2. Changing column properties
Configure the Properties of Column 1 in Spreadsheet 1 dialog as shown (Figure 3) with Type set to categorical and Attribute set to factor
Figure 3. Changing column 1 properties
Select OK
The samples names in column 1 are now black, indicating that they have been changed to a categorical variable. Next, we will add attributes for grouping the data.
From the RNA-seq workflow panel, select Add Sample Attributes to bring up the Add Sample Attributes dialog (Figure 4)
Figure 4. Add Sample Attributes dialog
Select Add a Categorical Attribute
Select OK to bring up the Create categorical attribute dialog
Creating a categorical sample attribute allows us to group samples. This is useful for designating samples as replicates, as members of an experimental group, or as sharing a phenotype of interest. In this tutorial, we have four different samples from different tissues and different donors, but to illustrate the available statistical analysis options, we need to divide the samples into two groups: muscle (Heart and Muscle) and not muscle (Brain and Liver).
Set Attribute name: as Tissue
Rename Group 1 to muscle and Group 2 to not muscle
Select and drag the samples from the Unassigned panel to the correct group panel (Figure 5)
Figure 5. Creating a categorical attribute
Select OK
Select No from the Add another attribute? dialog
Select Yes from the Save spreadsheet 1 dialog
The attribute will now appear as a new column in the RNA-seq spreadsheet with the heading Tissue and the groups muscle and not muscle.
The next available step in the Import panel of the RNA-seq workflow is Choose Sample ID Column_._ Verifying the correct column is designated the Sample ID becomes particularly important when data from multiple experiments is being combined.
Select Choose Sample ID Column from the Import panel of the RNA-Seq workflow
Select OK (Figure 6)
Figure 6. Choosing the correct column as Sample ID
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