Prediction Analysis for Microarrays, for the R package

  • R functions for PAM- software for carrying out sample classification from gene expression data,
    by the method of nearest shrunken centroids. You don't need to be familiar with R to start using PAM.
    What is R?

  • PAM is a simple, accurate and fast classifier, providing interpretable results for the biologist.

  • It has many novel features, including "heterogeneity analysis" for discriminating a diseased group from a normal one.

  • The methodology is described in Tibshirani, Hastie, Narashiman and Chu (2002):
    "Diagnosis of multiple cancer types by shrunken centroids of gene expression" . PNAS 2002 99:6567-6572 (May 14).

  • What is nearest shrunken centroids?

  • Some sample plots from PAM

  • PAM works under Windows and Unix/Linux. We have not yet tried our software on a Mac: R software is still evolving for the Mac. Given a working version of R, there is no reason why PAM shouldn't work.

    Installation guide and manual.

    Unix/Linux version

    Windows binary

    MAC OS X binary