Differential analysis - stjude/proteinpaint GitHub Wiki

The differential analysis app performs analyses tailored to each data type.

How this Plot Works

The plot is not available when:

1. Its not supported by the dataset.
2. The total number of samples for each group exceeds 4,000. If running gene expression analysis, the cutoff is 3,000 total samples.
3. There are overlapping samples in the groups.

How to Launch

Create at least one group in the Groups tab of the mass UI. Then create a custom variable from the Create variable using... button. Click on the new button for the custom term will appear below. Click on the option Differential analysis from the pop-up menu. Note the case and control groups are provided below the menu option.

Supported Analyses

Currently, only gene expression analysis is enabled.

Gene Expression

When performing differential gene expression analysis, both the volcano plot and gene set enrichment analysis plots are available. For more information, refer to the dedicated wiki pages for each plot.