affycomp.compfigs.auxiliary {affycomp} | R Documentation

## Auxiliary functions to create comparitive Figures

### 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.compfig5cdef(l, method.names = as.character(1:length(l)),
                      add.legend = TRUE, main = "Figure 5c", maxfp=100,
                      type=c("low","medlow","medhigh","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)

    affycomp.compfig5f(l, method.names = as.character(1:length(l)),
                      add.legend = TRUE, main = "Figure 5f", 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, 5e, and 5f. `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

    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))

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