affycomp.figures.auxiliary {affycomp} | R Documentation |
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.
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)
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). |
Read the vignette for more details on what each Figure is. You can read
assessSpikeIn
and assessDilution
to see
which assessments are needed.
Figures are produced.
Rafael A. Irizarry
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)