affycomp.compfigs.auxiliary: Auxiliary functions to create comparitive Figures

In affycomp: Graphics Toolbox for Assessment of Affymetrix Expression Measures

Description

These functions are auxiliary function to affycompPlot. These Figures are used to compare expression measures. They take lists with components created by the assessDilution and assessSpikeIn functions.

Usage

affycomp.compfig2(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 2")

affycomp.compfig3(l, method.names = as.character(1:length(l)),
                  main = "Figure 3")

affycomp.compfig4a(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, main = "Figure 4a")

affycomp.compfig4b(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, main = "Figure 4b")

affycomp.compfig4c(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, rotate=TRUE, main = "Figure 4c")

affycomp.compfig5a(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5a", maxfp=100)

affycomp.compfig5b(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5b", maxfp=100)

affycomp.compfig5cde(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5c", maxfp=100,
                  type=c("low","med","high"))

affycomp.compfig5c(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5c", maxfp=100)

affycomp.compfig5d(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5d", maxfp=100)

affycomp.compfig5e(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5e", maxfp=100)

Arguments

l	a list of lists with the necessary components to create the Figure. See details.
method.names	a character vector with the names of the expression measures methodologies being compared.
add.legend	logical. If TRUE a legend is added.
main	title of the Figure.
rotate	in the case of compfig4c one can eiher show the actual local slopes or the bias (local slope minus 1).
maxfp	range of the false positives in ROC will be from 0 to maxfp
type	compfig5cdef is the engine for 5c, 5d, and 5e. type tells is which of these 4 to run.

Details

These are similar to the functions defined in affycomp.figures.auxiliary. Main difference is that here you send lists with the result of the assessment functions as components.

Value

Figures are produced.

Author(s)

Rafael A. Irizarry

Examples

library(affycompData)
data(rma.assessment)
data(mas5.assessment)
affycomp.compfig2(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig3(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig4a(list(rma.assessment$Signal,mas5.assessment$Signal))
affycomp.compfig4b(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig5a(list(rma.assessment$FC,mas5.assessment$FC))
affycomp.compfig5b(list(rma.assessment$FC2,mas5.assessment$FC2))

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