Computational Biology and Bioinformatics

RMD_RUNS

The RMD_RUNS function will log10 transform peptide peak intensity, that is, peptide abundance data and determine if any LC-MS analyses (ie,runs) in a N x P peptide data set are statistical outliers. The statistical analysis is based on summarizing each LC-MS run as a vector of q=5 summary statistics which describe the peptide abundance distribution for a specific run; a N x q matrix is then analyzed using robust PCA to compute a robust estimate of the covariance matrix used in a the calculation of a robut Mahalanobis distance.

Requirements

  • Statistics Toolbox
    • Obtain from MathWorks, Inc.
  • PNNL Specific Functions
    • Cell2NumericVector.m
    • CreateSequentialNumbers.m
    • CorrelationMatrix.m
    • r_mad.m
  • K.U.Leuven Specific Functions (included in files)
    • robpca.m (Croux and Ruiz-Gazen, 2005)
    • L1median.m (Croux and Ruiz-Gazen, 2005)

Download

Download the zip folder and following these steps:

  • Extract .m files from the zip folder and either:
    • Add the destination file to your MatLab Path or,
    • Run in MatLab from the destination folder.
  • References

    Robust PCA

    • Croux, C. and Ruiz-Gazen, A (2005), "High breakdown estimatros for principal componets: the Projection-pursuit approach revisited", J Multivariate Analysis,95,206-226.
    • http://www.econ.kuleuven.be/public/NDBAE06/programs/#pca
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