Once you have created two or more alignments, you can perform a Differential Expression Analysis on those alignments. To do this, select “Create differential expression analysis” from the Actions menu.

Creating a Differential Expression Analysis is done in several steps, in the form of a wizard. It is required that all alignments in the differential expression analysis come from the same organism and were aligned using the same reference. The first step defines the overview of the analysis.

  1. You must specify the number of groups to be compared in the analysis, the organism, and the reference.
  2. Specify the type of analysis by selecting one or more of Gene, Exon, or Other. If you want to target the analysis to specific references names such as chromosomes 1,2, and X, in Include Reference Names enter “1,2,X”.
  3. Click “Define Group 1” to move to the next step of the wizard.

In the next steps of the analysis you will specify the alignments that make up each group and provide names for each group. If in (1) above you defined “Number of Groups” as being 2, there will be two pages of “Define group”, such as:

After you have defined all of the groups, the last step of the wizard is a “read-only” verification page where you can review your choices for the Differential Expression Analysis. After you accept your choices, the Differential Expression Analysis will be submitted to the cluster for processing. Processing on the cluster can take from a few minutes to a few hours, depending on system load and the number of samples analyzed.

When the Differential Expression Analysis has been completed, the Show Differential Expression Analysis page will look something like:

  1. GobyWeb provides it’s own browser for viewing the results of the Differential Expression Analysis, which will be shown below.
  2. If you want to browse and analyze the results offline, such as with JMP or Excel, you can download the TSV (tab separated values) file of the results.

Browsing the Results of the Differential Expression Analysis

By clicking “Browse Differential Analysis Results” on the “Show Differential Expression Analysis” page, you will be presented with a page similar to:

The data available here can be quite large, but GobyWeb makes it easy to deal with.

  1. The data are easy to filter. Just below the column headers are empty boxes. Click the (help ) button to learn about the different ways to filter the data.
  2. This text shows an overview of the analysis performed and the total number of rows of data in the analysis.
  3. The columns can be dragged to rearrange their order. If you double click a column header it will re-sort the table by this column.
  4. If you have filtered the data, this will show you the number of rows that meet your filter criteria.
  5. The Columns button allows you to select which columns are visible.
  6. The Export to TSV button allows you to export the data, as visible in the table. The export will respect the sorting, the visible columns, and the filtering that you have applied. This can be useful for other analysis you might want to perform in external tools such as JMP or Excel.