setGpar: Set graphical parameters for PLGEM fitting evaluation plots

Description

Function to set graphical parameters for PLGEM fitting evaluation plots produced by function plgem.fit.

Usage

setGpar(minLnM=NULL, maxLnM=NULL, minLnSD=NULL, maxLnSD=NULL, minRes=NULL, maxRes=NULL)

Arguments

minLnM

minimum 'ln(mean)' value in upper left plot.

maxLnM

maximum 'ln(mean)' value in upper left plot.

minLnSD

minimum 'ln(sd)' value in upper left plot.

maxLnSD

maximum 'ln(sd)' value in upper left plot.

minRes

minimum 'residual' value in upper right plot.

maxRes

maximum 'residual' value in upper right plot.

Value

minLnM: minimum 'ln(mean)' value in upper left plot.
maxLnM: maximum 'ln(mean)' value in upper left plot.
minLnSD: minimum 'ln(sd)' value in upper left plot.
maxLnSD: maximum 'ln(sd)' value in upper left plot.
minRes: minimum 'residual' value in upper right plot.
maxRes: maximum 'residual' value in upper right plot.

Details

A call to setGpar() is the recommended way to set graphical parameters in plgem.fit. If parameters are left unspecified, suitable defaults will be found by plgem.fit.

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. 2008 Apr; 7(4):631-44; http://www.mcponline.org/cgi/content/abstract/7/4/631.

Examples

Run this code

  setGpar(minLnM=-1, maxLnM=8)

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