PaGE 5.0 Example - simulated dataset

This illustrates running PaGE on a simple example. The data file consists of

Click here to see the dataset. Note that the header is formatted according to the two condition convention. The first 50 genes, with ID's 0-49, are differentially expressed across the four conditions. The rest are generated with the same distribution across all 16 columns.

  • There is a mock file which maps ID's to names, so we will tell PaGE that using the option id2info.
    We now start up PaGE with the following commandline command:
    > java -classpath "jh.jar;PaGE.jar" -Xmx512m page.PaGE in Windows PCs
    or 
    > java -classpath "jh.jar:PaGE.jar" -Xmx512m page.PaGE in Linux or Mac PCs
    
    Make sure the command prompt is in the directory containing the PaGE.jar and jh.jar files. You may have to include the full path to the java executable if it is not in your classpath. If you do not have java installed, go to www.sun.com and get J2SE 1.4.2. If everything is working properly, this is what should come up on the screen:
     

    PaGE has started up. We start by choosing "new analysis type" from the "File" menu
     

    We will now be asked a series of questions about our data and study design. Our data for this example is one-channel, unlogged, unpaired data.

    After answering these questions the analysis type has been fully defined. You next have to input the data.

    Inputting the data

    Choose menu item Data Open Data file

    You should see a file browser that will allow you to find the data file on your disk.

    Including gene information and links in the output

    Choose menu item Data Open id2info file

    This allows you to enter a file of gene descriptions which will be included in the results file.

    Choose menu item Data Open id2url file

    This allows you to enter a file of URLs, to be included in the results file as links.

    It will now report some parameters regarding the input file. You should check that this agrees with what you expect.

    We will leave the Options as their defaults. We are now ready to run PaGE. We will run it using the t-statistic. Choose Run PaGE by t-stat.

    PaGE will now ask for the level confidence, and the reference group.

    The default value for the level confidence is .75 and the default reference group is group 0. We will use the defaults.

    Finally it will ask if we want to run the algoirithm on the log transformed data. We will choose unlogged.

    PaGE will now work through the permutations, after which the results will appear in a text box on the screen.

    These results give a tab delimited view. Genes break down into lists for each level. Each gene is shown with its confidence and the value of the statistic. A more comprehensive view is obtained by saving the results to HTML. To do this choose Save Result.

    Choose "Save as HTML file"

    A file browser will appear. Give the file a name. We will call it example1_results

    The file example1_results.html is written. You'll notice PaGE also write a file called  example1_results_intensity.html  which contains intensity information linked to from the main report. PaGE will write several auxiliary files if the output is large.

    At the top of the report some information is given specific to this run:

    Now starts the main part of the report that gives the actual 42 genes found. Each gene is reported with