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Last data update: 2014.03.03

R: Assessment Plots

affycompPlot

R Documentation

Assessment Plots

Description

Function that makes assessment plot

Usage

affycompPlot(...,assessment.list=NULL,method.names=NULL,
             figure1.xlim=c(-4,15),figure1.ylim=c(-10,12),
             figure1b.xlim=c(-2,14),figure1b.ylim=c(-6,5),
             figure6a.xlim=c(-12,12),figure6a.ylim=c(-12,12),
             figure6b.xlim=c(-3,3),figure6b.ylim=c(-6,6))

affycomp.compfigs(l, method.names = NULL, figure1.xlim = c(-4, 15),
                 figure1.ylim = c(-10, 12), figure1b.xlim = c(-4, 15),
                 figure1b.ylim = c(-4, 4), figure6a.xlim = c(-12, 12),
                 figure6a.ylim = c(-12, 12), figure6b.xlim = c(-3, 3),
                 figure6b.ylim = c(-6, 6))
affycomp.figures(l)
affycomp.figure.calls(what)
affycomp.compfigs.calls(what)

Arguments

`...`	lists produced by the assessment functions (one for each method) separated by commas.
`assessment.list`	Alternatively, one can also send a list of lists produced by one of the assessment functions

`method.names`	A character vector with the names of the epxression measure methodology.
`figure1.xlim`	x-axis lim used for the plots in Figure 1.
`figure1.ylim`	y-axis lim used for the plots in Figure 1.
`figure1b.xlim`	x-axis lim used for the plots in Figure 1b.
`figure1b.ylim`	y-axis lim used for the plots in Figure 1b.
`figure6a.xlim`	x-axis lim used for the plots in Figure 6a.
`figure6a.ylim`	y-axis lim used for the plots in Figure 6a.
`figure6b.xlim`	x-axis lim used for the plots in Figure 6b.
`figure6b.ylim`	y-axis lim used for the plots in Figure 6b.
`l`	list with assessment lists as components.
`what`	a dummy variable to know what function call to create.

Details

Read the vignette for more details on what each Figure is. Once an assessment is used this function knows what to do. You can call any of the assessment functions described in assessSpikeIn, assessDilution and assessSD.

affycomp.figures, affycomp.figure.calls, affycomp.compfigs.calls are auxiliary functions.

Value

Figures are produced.

Author(s)

Rafael A. Irizarry

Examples

library(affycompData)
data(rma.assessment)
data(mas5.assessment)
affycompPlot(rma.assessment,mas5.assessment)
affycompPlot(rma.assessment$FC)
affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
affycompPlot(rma.assessment$Signal,mas5.assessment$Signal)
affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
affycompPlot(rma.assessment$FC2,mas5.assessment$FC2)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(affycomp)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affycomp/affycompPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: affycompPlot
> ### Title: Assessment Plots
> ### Aliases: affycompPlot affycomp.figure.calls affycomp.compfigs.calls
> ###   affycomp.figures affycomp.compfigs
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library(affycompData)
> data(rma.assessment)
> data(mas5.assessment)
> affycompPlot(rma.assessment,mas5.assessment)
> affycompPlot(rma.assessment$FC)
> affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
> affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
> affycompPlot(rma.assessment$Signal,mas5.assessment$Signal)
> affycompPlot(rma.assessment$Dilution,mas5.assessment$Dilution)
> affycompPlot(rma.assessment$FC2,mas5.assessment$FC2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>