densityplot: Density plots of log2 intensity values

In MmPalateMiRNA: Murine Palate miRNA Expression Analysis

Description

Plots the estimated density of log2 intensity values for two-color microarrays

Usage

## S4 method for signature 'RGList,missing'
densityplot(
    x,
    channel=c("G", "R"),
    group=NULL,
    subset=NULL, 
    ...)

## S4 method for signature 'list,missing'
densityplot(
    x,
    channel=c("G", "R"),
    group=NULL,
    subset=NULL, 
    ...)

Arguments

x	Either an RGList object, or a list containing MAList and/or NChannelSet objects
channel	The channel to use for calculating distances, one of either "G" (green or control channel) or "R" (red or experimental channel)
group	An optional character string specifying the name of a factor to create separate panel displays, which must be in x$genes (for RGList objects)
subset	An optional character vector specifying the which levels of group to use in creating separate panel displays
...	arguments to pass to densityplot

Methods

signature(x = "RGList", data = "missing")

For RGList objects, separate panel displays can be produced for different types of probes, as determined by the group argument.

signature(x = "list", data = "missing")

The method for list objects is intended to work with lists of normalized data sets, as either MAList or NChannelSet objects. This method will produce separate panel displays for each normalized data set, additionally subsetted by the group argument if supplied. The useOuterStrips function in the latticeExtra package can be used for ‘outer’ strip labels in the latter case.

References

D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, and M. Tewari. Quality assessment and data analysis for microRNA expression arrays. Nucleic Acids Res, 37(2):e17, 2009.

See Also

levelplot for pairwise distance plots between arrays, MADvsMedianPlot for median absolute deviation versus median plots, and MAplot for MA plots

Examples

data(PalateData)
res <- densityplot(PalateData, channel="G", group="probe.type", 
                   subset = c("Other miRNAs",   "MMU miRNAs", "Control"), 
                   col=rep(1:3, each=3), lty=rep(1:3, 3), 
                   key = list(lines=list(col=rep(1:3, each=3), lty=rep(1:3, 3)), 
                     columns=3))
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, 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

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.