M versus A plot

Description

A matrix of M vs. A plots of each pair (ip, control) is produced.

Usage

plotMA(eSet, ip=NULL, control=NULL, col=NULL)

Arguments

Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

See Also

ma.plot

Examples

##
mat <- matrix(rnorm(1000000), ncol=4)
colnames(mat) <- c("Sample1", "Sample2", "Sample3", "Sample4")
mat[,1] <- mat[,1]^2
plotMA(mat, c(TRUE, FALSE, TRUE, FALSE), c(FALSE, TRUE, FALSE, TRUE))

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.
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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(Starr)
Loading required package: Ringo
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")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
Loading required package: affy

Attaching package: 'affy'

The following object is masked from 'package:Ringo':

    probes

Loading required package: affxparser

Attaching package: 'Starr'

The following object is masked from 'package:affy':

    plotDensity

The following object is masked from 'package:limma':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Starr/plot.ma.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMA
> ### Title: M versus A plot
> ### Aliases: plotMA
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ##
> mat <- matrix(rnorm(1000000), ncol=4)
> colnames(mat) <- c("Sample1", "Sample2", "Sample3", "Sample4")
> mat[,1] <- mat[,1]^2
> plotMA(mat, c(TRUE, FALSE, TRUE, FALSE), c(FALSE, TRUE, FALSE, TRUE))
Plotting Sample1vsSample2  Sample1vsSample4  Sample3vsSample2  Sample3vsSample4  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>