MAplot: Relative M vs. A plots

In affy: Methods for Affymetrix Oligonucleotide Arrays

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)
}

Example output

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, which, which.max, which.min

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")'.

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Loading required package: affydata
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'affydata'

affy documentation built on Nov. 8, 2020, 8:18 p.m.