mva.pairs: M vs. A Matrix

In affy: Methods for Affymetrix Oligonucleotide Arrays

Description

A matrix of M vs. A plots is produced. Plots are made on the upper triangle and the IQR of the Ms are displayed in the lower triangle

Usage

mva.pairs(x, labels=colnames(x), log.it=TRUE,span=2/3,family.loess="gaussian",
          digits=3,line.col=2,main="MVA plot",cex=2,...)

Arguments

x	a matrix containing the chip data in the columns.
labels	the names of the variables.
log.it	logical. If TRUE, uses log scale.
span	span to be used for loess fit.
family.loess	"gaussian" or "symmetric" as in loess.
digits	number of digits to use in the display of IQR.
line.col	color of the loess line.
main	an overall title for the plot.
cex	size for text.
...	graphical parameters can be given as arguments to mva.plot

.

See Also

pairs

Examples

    x <- matrix(rnorm(4000),1000,4)
    x[,1] <- x[,1]^2
    dimnames(x) <- list(NULL,c("chip 1","chip 2","chip 3","chip 4"))
    mva.pairs(x,log=FALSE,main="example")

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, 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'

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