MAplot of a ExpressionSet object

Description

Creating pairwise MAplot of sample intensities in a ExpressionSet object

Usage

## S4 method for signature 'ExpressionSet'
MAplot(object, ..., smoothScatter = FALSE, logMode = TRUE, subset = 5000, main = NULL)

Arguments

Details

To increase the plot efficiency, by default, we only plot RANDOMLY selected subset of points (based on parameter "subset"). If users want to plot all the points, they can set the parameter "subset = NULL". When smoothScatter is set as TRUE, the subsetting will be suppressed because smoothScatter function has good plot efficiency for large number of points.

See Also

LumiBatch-class, MAplot

Examples

## load example data
data(example.lumi)

MAplot(example.lumi)

MAplot(example.lumi, smoothScatter=TRUE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(lumi)
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/MAplot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAplot-methods
> ### Title: MAplot of a ExpressionSet object
> ### Aliases: MAplot-methods MAplot MAplot.ExpressionSet
> ###   MAplot,ExpressionSet-method
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumi)
> 
> MAplot(example.lumi)
> 
> MAplot(example.lumi, smoothScatter=TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>