ComparativeMarkerSelectionViewer (v9)

The ComparativeMarkerSelectionViewer provides tools for reviewing and working with ComparativeMarkerSelection results. These tools include plots, a data table, expression profiles, filters, and creating dataset and feature list files. (A feature list is a text file with one feature per line.)

ComparativeMarkerSelectionViewer is an interactive tool. For non-interactive access to annotations, heatmaps, and creation of datasets and features lists, see the HeatMapImage, and ExtractComparativeMarkerSelection modules.

Heatmap/Plots

Heatmap and plots are displayed in the upper portion of the viewer. Use the View menu to select the plot to display:

• Heatmap (initially displayed) is a heatmap of the expression values sorted by the test statistic value.
• Upregulated Features plots the descending test statistic values versus features sorted by the test statistic value. This plot is useful for visualizing the number of features that have a positive and negative test statistic value in each class.
• Custom plots  provide a pair-wise comparison of different statistics. To display custom plots click View > Custom Plot. To compare different significance measures: use the drop-down lists below the plot to select the measures to display on the X and Y axes and click Update. The viewer updates the plot and to reflect the new comparison.
• Histograms show the null distributions for each measure of significance.
• Use the following File> Save Image menu item to save the heatmap or plot. When saving a heatmap the currently visible rows will be saved by default. Optionally the entire heatmap can be saved by selecting include all features and samples. There is a limit on the size of the heatmap when saving in PNG format. The limit is roughly (number of features * number of samples <= 3580000).

Zoom in/out of plots

Use the mouse to click-and-drag over the plot area to zoom in.

Use the Reset button (upper right of plot) to return the zoom to the default level. 

Note: Zoom in/out not available for heatmap.

Data Table

The table in the lower portion of the viewer lists the ComparativeMarkerSelection results. For a description of each column, see the ComparativeMarkerSelection documentation. By default, the features in the table are ordered by score. To reorder the features, click the title of the key column; for example, to order features by rank, click Rank.  

To choose which columns are shown in the table, click the Column Show/Hide toggle icon in the top-left corner of the table, just to the left of the search bar:

Using File>Save Table, you can export the table in tab delimited format for use in external programs such as Excel. This will result in a tab-delimited file with the contents of the table, leaving out any items excluded due to filters or columns hidden through the Column Show/Hide toggle.

Expression Profiles

The expression profile for a feature plots expression value per sample. A heatmap shows the same information, but color codes the expression values from red for the highest expression values through blue for lowest expression values. 

To display an expression profile:

1. Select one feature from the data table.
2. Click View>Profile. 

Filters

Use filters to display only features that you are interested in:

1. Select Edit>Filter Features>Create/Edit Filters. The Filter Features window appears.
2. In the Filter Features window, set your filtering criteria and click OK. The viewer will then only show those features that meet your criteria.
3. To redisplay all features, select Edit>Remove All Filters.

Creating Datasets/Feature Lists

You can use the viewer to create a new dataset in GCT format or a feature list (a text file with one feature per line) containing a listing of the selected features in the table in from the ComparativeMarkerSelection results:

1. Select the desired features from the table.
2. Select File>Save Dataset or File>Save Feature List. A window appears.
3. Choose a location and name for the new dataset/feature list.
4. Click OK to save the new data set/feature.

References

Gould et al. Comparative Gene Marker Selection suite. Bioinformatics Advance Access published on May 18, 2006, DOI 10.1093/bioinformatics/btl196.

Parameters

Name	Description
comparative marker selection filename *	The output from ComparativeMarkerSelection
dataset filename *	The dataset file used as input to ComparativeMarkerSelection

* - required

Input Files

1. comparative marker selection filename
   The output file from ComparativeMarkerSelection in ODF format.
2. dataset filename
   The dataset file used as input to ComparativeMarkerSelection in GCT format.

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javascript

CPU Type:
any

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