Compute the Mahalanobis distance of each sample from the center of an N-dimensional principal component space.
object of class
integer scalar specifying the number of components to use when assessing QC.
The theory says that, under the null hypothesis that all samples arise from the same multivariate normal distribution, the distance from the center of a D-dimensional principal component space should follow a chi-squared distribution with D degrees of freedom. This theory lets us compute p-values associated with the Mahalanobis distances for each sample. This method can be used for quality control or outlier identification.
Returns a data frame containing two columns, with the rows
corresponding to the columns of the original data set on which PCA was
performed. First column is the chi-squared statistic, with
degrees of freedom. Second column is the associated p-value.
Kevin R. Coombes [email protected]
Coombes KR, et al.
Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin Chem 2003; 49:1615-23.
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Loading required package: cluster Loading required package: oompaBase statistic p.value CL2005060326AA 11.609371 3.013402e-03 CL2005060327AA 9.899135 7.086472e-03 CL2005060332AA 10.040577 6.602621e-03 CL2005060339AA 19.491723 5.853643e-05 CL2005060352AA 9.857223 7.236545e-03 CL2005060355AA 13.179456 1.374414e-03 CL2005060360AA 13.388629 1.237930e-03
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