Exploring gene set details

From the Output Panel (table or tree), you can double-click on a gene set row to pop up a new window showing the details for the gene set. If you have done multiple analyses, click on the p-value for the specific gene set you wish to view. If you have not done any analysis, you will still see the window. After double-clicking, you will see a new window.

A typical window will look like this

There are a few things to note:

• If you have done an analysis, then the relevant gene score file will be defined, and the probe scores for the probes in the gene set will be displayed. If you have no current analyses, then the last gene score file you used will be selected for showing probe scores. If you have not selected a gene score file, no gene scores will be displayed (you will see "NaN" for "not a number" instead).
• If you have previously loaded your raw expression data, the window will include a visualization of the data. If you have not, you will be prompted to choose a data file. The file format must follow the rules described here. If you choose not to load a data file at this time, you will not be asked again during this session. If you want to see raw data, you can set the data set from a menu option.
• You can open as many visualization windows as you like, including multiple windows for the same gene set.
• You can switch the data set or gene score file to view. This setting is remembered across sessions. If you set these files in the Analysis wizard, that setting will be used. The settings you make here are also remembered.
• The title of the window shows the gene set name, size and the p-value, if there is one

The non-data columns are as follows:

• Probe - the identifier supplied by the array manufacturer, read in from the annotation file. In this example, this is an Affymetrix array.
• Score - the user-supplied gene score (if you have supplied one). This value is loaded from the "gene scores" file. Probes which were present in the array design, but not used for analysis due to lack of a gene score, are shown with a score of "NaN" (not a number).
• Score (visual) - a graph showing the scores graphically. The blue line represents the scores. The grey line shows the expected distribution under the null hypothesis and assuming independence (this only works if the values are p values).
• Symbol - the official gene symbol as supplied in the annotation file, with hyperlinks to a web site of your choosing.  You can change the target URL as described here . 
• Name - the gene name as supplied in the annotation file.
  

Image controls

• Sorting: Clicking on any column (including the raw data column) headers result in sorting of the view.
• Contrast: You can adjust the color range (contrast) and cell width for the color map.

  
  
  

• Resize the columns in the image view. Use this to "zoom out" to make the image fit horizontally on your screen.
• Using the "View" menu, you can switch between different preset color maps and choose normalize or non-normalized data for viewing.

  
  
  

  
  
  

Changing the hyperlinks

When you click on a gene symbol, your web browser will be opened to a web site of your choosing. The preset is the NCBI "Gene" database, but you can change this using the "Options->Change gene name URL" menu item:

Using this requires that you know the URL (web address) for a gene. Just replace the term you would normally put in the URL with two "at" symbols ("@@"). They will be replaced with the Gene Symbol.

For details and some examples, see this page.

Changing the data set

You can switch data sets (or define one if you have never loaded one) viewed in the heatmap by selecting the "Options->Change data set". Here's an example where we switched:

Note: Naturally, if you switch to a data set that uses a different microarray design, the results might not make much sense. Note that the gene scores displayed are always the ones you used for the last analysis (or the run you double-clicked on) to get this window)

Note: If you switch data sets, the setting is "sticky": all new visualization windows you open will use this data set, until you switch back.

Changing the gene score file

This is similar to the function for setting the raw data file.

Saving the data and/or image

Using the "File" menu, you can save the data shown, in text or image formats:

Here is an example of the resulting image, which is in PNG format:

You can also save the data using the "File...Save data..." menu option:

A sample resulting file for the data above is here. In this case we had the "include annotations" but not "normalize" checked. This file can be loaded into Excel or a simliar program for further analysis.