plgem.pValue {plgem}R Documentation

Computation of PLGEM p-values

Description

This function computes p-values for observed PLGEM signal-to-noise ratio (STN) values (typically obtained via a call to plgem.obsStn) from resampled STN values (typically obtained via a call to plgem.resampledStn).

Usage

  plgem.pValue(observedStn, plgemResampledStn, verbose=FALSE)

Arguments

observedStn matrix of observed PLGEM STN values; output of plgem.obsStn.
plgemResampledStn list; output of plgem.resampledStn.
verbose logical; if TRUE, comments are printed out while running.

Details

The p-value of each given observed STN value is computed based on the quantile that the given value occupies in the corresponding distribution of resampled PLGEM STN values, based on the following relationship:

p-value = min(2*quantile, 2*(1-quantile))

Value

plgem.pValue returns a matrix with the same dimensions and dimnames as the input ‘observedStn’, where each entry represents the p-value of the corresponding observed PLGEM STN value.

Author(s)

Mattia Pelizzola mattia.pelizzola@gmail.com

Norman Pavelka nxp@stowers-institute.org

References

Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P. A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics. 2004 Dec 17;5:203; http://www.biomedcentral.com/1471-2105/5/203

Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics. 2007 Nov 19; http://www.mcponline.org/cgi/content/abstract/M700240-MCP200v1

See Also

plgem.fit, plgem.obsStn, plgem.resampledStn, run.plgem

Examples

  data(LPSeset)
  LPSfit <- plgem.fit(data=LPSeset)
  LPSobsStn <- plgem.obsStn(data=LPSeset, plgemFit=LPSfit)
  head(LPSobsStn)
  set.seed(123)
  LPSresampledStn <- plgem.resampledStn(data=LPSeset, plgemFit=LPSfit)
  LPSpValues <- plgem.pValue(LPSobsStn, LPSresampledStn)
  head(LPSpValues)

[Package plgem version 1.14.0 Index]