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Last data update: 2014.03.03

R: Relative M vs. A plots

MAplot

R Documentation

Relative M vs. A plots

Description

Create boxplots of M or M vs A plots. Where M is determined relative to a specified chip or to a pseudo-median reference chip.

Usage

MAplot(object,...)
Mbox(object,...)
ma.plot(A, M, subset = sample(1:length(M), min(c(10000, length(M)))),
        show.statistics = TRUE, span = 2/3, family.loess = "gaussian",
        cex = 2, plot.method = c("normal","smoothScatter","add"),
        add.loess = TRUE, lwd = 1, lty = 1, loess.col = "red", ...)

Arguments

`object`	an `AffyBatch-class`.
`...`	additional parameters for the routine.
`A`	a vector to plot along the horizontal axis.
`M`	a vector to plot along vertical axis.
`subset`	a set of indices to use when drawing the loess curve.
`show.statistics`	logical. If TRUE, some summary statistics of the M values are drawn.
`span`	span to be used for loess fit.
`family.loess`	`"guassian"` or `"symmetric"` as in `loess`.
`cex`	size of text when writing summary statistics on plot.
`plot.method`	a string specifying how the plot is to be drawn. `"normal"` plots points, `"smoothScatter"` uses the `smoothScatter` function. Specifying `"add"` means that the MAplot should be added to the current plot.
`add.loess`	add a loess line to the plot.
`lwd`	width of loess line.
`lty`	line type for loess line.
`loess.col`	color for loess line.

See Also

mva.pairs

Examples

if (require(affydata)) {
   data(Dilution)
   MAplot(Dilution)
   Mbox(Dilution)
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(affy)
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

Loading required package: Biobase
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/affy/MAplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAplot
> ### Title: Relative M vs. A plots
> ### Aliases: ma.plot Mbox MAplot Mbox,AffyBatch-method
> ###   MAplot,AffyBatch-method
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require(affydata)) {
+    data(Dilution)
+    MAplot(Dilution)
+    Mbox(Dilution)
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>