Differential expression analysis can be used to compare cell types. Here, we will compare malignant and oligodendrocyte cells to identify genes differentially regulated in malignant cells from the Oligodendroglioma subtype. This comparison is of interest because malignant cells in Oligodendroglioma are thought to originate from oligodendrocytes. 

Normalize counts

To eliminate any zero values in the data set, add a small offset. 

• Select the Classified groups (green) data node
• Select Normalization from the Normalization and scaling section of the task menu

The normalization options for single-cell RNA-Seq data are the same as for pooled or bulk RNA-Seq data.

• Drag and drop Add from the left panel to the right panel
• Set to 0.0001
• Select Finish

Identify differentially expressed genes

• Select the Normalized counts (green) data node
• Select Detect differential expression (GSA) 

The configuration options include cell-level attributes. Some of these are inherited from the sample level, like Type. Here, we want to compare only cells of a particular type from particular classification so we will include Type and Classification. 

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