MAplot: MA plot

In MmPalateMiRNA: Murine Palate miRNA Expression Analysis

Description

Plots of the log2 expression ratios (M values) versus the mean log2 expression values (A values) for each probe for each array.

Usage

MAplot(x, ...)

## S4 method for signature 'MAList'
MAplot(
    x,
    ...)

## S4 method for signature 'NChannelSet'
MAplot(
    x,
    ...)

Arguments

x	Either an MAList object or an NChannelSet object
...	arguments to pass to xyplot

Details

The so-called "MA" plot can be used to evaluate whether their is a bias associated with overall intenstity level for each array. Loess smoothed regression lines are superimposed on each plot to demonstrate the trend.

Methods

signature(x = "MAList")

M and A values are stored as matrices in x

signature(x = "NChannelSet")

M and A values are calculated from the R and G matrices returned by assayData(x)

See Also

densityplot for density plots of log2 intensity values, levelplot for pairwise distance plots between arrays, and MADvsMedianPlot for median absolute deviation versus median plots.

Examples

data(PalateData)
reducedSet <- filterArray(PalateData, keep=c("MIR", "LET", "POSCON", "CALIB"),
                          frac=1.1, number=3, reps=4)
ndata.quantile <- normalizeBetweenArrays(reducedSet, method="quantile")
res <- MAplot(ndata.quantile)
print(res)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: xtable
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: statmod
Loading required package: lattice
Loading required package: vsn
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'

MmPalateMiRNA documentation built on April 28, 2020, 7:54 p.m.