affycomp.figures.auxiliary: Auxiliary functions to create Figures

In affycomp: Graphics Toolbox for Assessment of Affymetrix Expression Measures

Description

These functions are auxiliary function to affycompPlot. These Figures are used to assess an expression measure. They take components created by the assessDilution and assessSpikeIn functions.

Usage

affycomp.figure1(l,main="Figure 1",xlim=NULL,ylim=NULL)
affycomp.figure1b(l,main="Figure 1b",xlim=NULL,ylim=NULL,cex=0.85,all=FALSE)
affycomp.figure2(l,main="Figure 2")
affycomp.figure2b(l,main="Figure 2b")
affycomp.figure3(l, main = "Figure 3")
affycomp.figure4a(l, main = "Figure 4a",equal.lims=FALSE)
affycomp.figure4b(l, main = "Figure 4b")
affycomp.figure4c(l, rotate=TRUE, main = "Figure 4c")
affycomp.figure5a(l, main = "Figure 5a",maxfp=100)
affycomp.figure5b(l, main = "Figure 5b",maxfp=100)
affycomp.figure5c(l, main = "Figure 5c",maxfp=100)
affycomp.figure5d(l, main = "Figure 5d",maxfp=100)
affycomp.figure5e(l, main = "Figure 5e",maxfp=100)
affycomp.figure6a(l, main = "Figure 6a",xlim = NULL, ylim = NULL)
affycomp.figure6b(l, main = "Figure 6b",xlim = NULL, ylim = NULL)

Arguments

l	A list with the necessary components to create the Figure. See details.
main	Title for the Figure.
maxfp	range of the false positives in ROC will be from 0 to maxfp
xlim	x-axis limits.
ylim	y-axis limits.
cex	size of numbers in figure 1b.
all	logical. If TRUE all spikeins are shown. Otherwise, only those resulting in smaller, realistic, fold changes are shown.
equal.lims	logical. If TRUE the limits of x-axis and y-axis will have same range.
rotate	in the case of compfig4c one can eiher show the actual local slopes or the bias (local slope minus 1).

Details

Read the vignette for more details on what each Figure is. You can read assessSpikeIn and assessDilution to see which assessments are needed.

Value

Figures are produced.

Author(s)

Rafael A. Irizarry

Examples

library(affycompData)
data(rma.assessment)
affycomp.figure1(rma.assessment$MA)
affycomp.figure2(rma.assessment$Dilution)
affycomp.figure3(rma.assessment$Dilution)
affycomp.figure4a(rma.assessment$Signal)
affycomp.figure4b(rma.assessment$Dilution)
affycomp.figure5a(rma.assessment$FC)
affycomp.figure5b(rma.assessment$FC2)
affycomp.figure6a(rma.assessment$FC)
affycomp.figure6b(rma.assessment$FC)

affycomp documentation built on Nov. 8, 2020, 5:55 p.m.