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Metagene Projection paper R code and datasets README

The 3 zip files next too this readme file:

MP_leukemia1_example_R_code_and_datasets.zip
MP_leukemia2_example_R_code_and_datasets.zip
MP_lung_example_R_code_and_datasets.zip

contain each a complete copy of the R code and relevant datasets for
each of the examples in the paper:

Metagene projection for cross-platform, cross-species characterization 
of global transcriptional states. P. Tamayo, D. Scanfeld, B. L. Ebert, 
M. A. Gillette, C. W. M. Roberts, and J.P. Mesirov. PNAS 104:
5959-5964 2007. 
http://www.pnas.org/cgi/content/abstract/0701068104v1
 
To re-run the examples (and eventually use the code on your datasets) do the following:

 * Download the zip files to your local computer:  (you can download only one of them if you want)
    MP_leukemia1_example_R_code_and_datasets.zip
    MP_leukemia2_example_R_code_and_datasets.zip
    MP_lung_example_R_code_and_datasets.zip
 
 * Check that you have R installed (at least release 2.2.1) in your local computer. 
   If you don't have R you can get it from www.r-project.org

  * The first leukemia example (Figs 2-3 in the paper) is included in file: 
          MP_leukemia1_example_R_code_and_datasets.zip
    After unzipping the file in a new empty directory use a text 
    editor to modify the file "Leukemia1.R"  and replace the pathnames 
    to the proper directories in your local computer. Then cut and
    paste the content of "Leukemia1.R"  into the R GUI. This is the
    main E script that defines the parameters and files for the
    run. It sources the file ``MP.library.R'' which contains the
    actual R code that implements the functions to perform the metagene
    projection, read the datsets etc. The program should run for
    about a couple of minutes and then produce plots on the screen and in
    files under the directory specified by "output.dir". There is more
    detailed documentation at the top and thru the file "Leukemia1.R".
    The zip file contain all the datasets that are needed for that example.

  * To run the second leukemia example (Fig 4 in the paper) follow the
  same procedure but use the file "Leukemi2.R" from the zip file:
       MP_leukemia2_example_R_code_and_datasets.zip
    In that file there are all the datasets needed for the
    example. There are also two other R script: "Leukemia2.ALL.R" and
    "Leukemia2.AML.R" that run the example using only the ALL and AML
    samples respectively.

  * To run the lung example (Fig 5A in the paper) follow the same
  procedure but use the file "Lung.1.R" from the zip file:
         MP_lung_example_R_code_and_datasets.zip
    In that file there are all the datasets needed for the
    example. There is also an additional script "Lung.2.R" that runs
    the case with the "normal" metagene set to zero and without the
    normal samples (Fig 5B in the paper).

  If you have questions or comments send them to tamayo@broad.mit.edu.
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