07/16/2020
Differential Expression Results
- Contents
- Results Overview
- Differential Expression - Results
- Differential Expression Results - Full Table
| Legend | Name | Description |
|---|---|---|
| A | Summary table | List of differentially expressed genes for each comparison result in this analysis. |
| B | Full table | Displays the full table of DE analysis results in a new window. |
| C | Selected set of comparisons | Selects a set among the comparison groups. In multiple comparison type, this separates the comparison modes (e.g. "crossed" from "lateral", since both are used in "combinatorial" mode). In temporal analysis, this box separates between temporal comparison sequences. |
| D | Summary results plot | Chart that summarizes the propotion between over- and under-expressed genes. This is represented as a bar char in multiple comparison type, and as a stacked chart in temporal comparison type. |
| E | Plot legend | Plot legend describing the plot elements. |
| F | Save plot image | Saves the current chart to an external image. |
Differential Expression - Results
| Legend | Name | Description |
|---|---|---|
| A | Projects | Registers the comparison results inside a project, so that it can be queried afterwards. This option is not available when confering the results in a unloaded session. |
| B | Generate R Code | Generates the R source code for the current session in addition to the commands used in the differential expression analysis. |
| C | Gene Ontology Analysis | Opens a dialog to initialize the Gene Ontology analysis. |
Differential Expression Results - Full Table
| Legend | Name | Description |
|---|---|---|
| A | List of Comparison Results | Tables of comparison results, which can be selected by the mouse click. |
| B | Pin first column | Keeps the first column in the view |
| C | Show/Hide columns | Show or hide certain columns |
| D | Order columns | Sort the data based on the values from a column. |
| E | Split/Join column entries with composed fields | Splits the values containing a separator, resulting in a multifield column. |
| F | Current results table | Table being displayed. |
| G | Filter | Filters the table rows based on the user's criteria. |
| H | Applied filters | Shows already applied filters. |
| I | Export table | Exports the current table to an external file (main button), or all tables to a output directory (side button, "Export All Tables"). |
| J | Overview plot | Plot that summarizes the amount of differentially expressed genes based on the current filtered results. |
| Legend | Name | Description |
|---|---|---|
| A | Proportion (Pie Chart) |
| Legend | Name | Description |
|---|---|---|
| A | Scatter Plot | |
| B | Mouse cursor coordinates | |
| C | Displayed attribute in Tooltip |
| Legend | Name | Description |
|---|---|---|
| A | Volcano plot |
Remarks
Each comparison result has the following columns:
- logFC: estimate of the log2-fold-change between Experimental and Control (or next step vs last step in temporal comparisons);
- AveExpr: average log2-expression for the probe over all arrays and channels;
- t: moderated t-statistic;
- P.Value: raw p-value
- adj.P.Value: adjusted p-value or q-value
- B: log-odds that the gene is differentially expressed (omitted for TREAT option)