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Archived Comments for: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer

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  1. A problem in the provided numbers

    Ozgun Babur, Memorial Sloan Kettering Cancer Center

    29 August 2015

    Dear authors of CoMEt,

    I am having hard time replicating your simulations. There is a mismatch of numbers in your article.

    The steps of generating the simulated datasets is given in Additional File 1, section 3. The text says the average number of genes in the simulated datasets (after minimum alteration filtering) is 276. However, when I repeat this procedure, I get an average of 9 genes.

    Either the given parameters are wrong, or the average is wrong. You can also see this mismatch without writing any code. The procedure starts with the initial number of genes m=100, and the minimum alteration filtering can only reduce this number. This means the average number of genes has to be equal or less than m.

    Can you please clarify this? I need to pass this step to be able to replicate your simulations.


    Ozgun Babur

    Competing interests

    I am a developer of Mutex
  2. Response to: "A problem in the provided numbers"

    Mark Leiserson, Brown University

    12 September 2015

    Thank you, Ozgun, for pointing out the discrepancy in the number m of genes in the simluations. The number m=100 in the Additional File 1 is a typo. We used m=20,000.

    Competing interests

    None declared