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))