| affycomp.compfigs.auxiliary {affycomp} | R Documentation |
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.
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)
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. |
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.
Figures are produced.
Rafael A. Irizarry
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))