image: Display a pseudo-image of a microarray chip

In oligo: Preprocessing tools for oligonucleotide arrays

Description

Produces a pseudo-image (graphics::image) for each sample.

Usage

## S4 method for signature 'FeatureSet'
image(x, which, transfo=log2, ...)

## S4 method for signature 'PLMset'
image(x, which=0,
                   type=c("weights","resids", "pos.resids","neg.resids","sign.resids"),
                   use.log=TRUE, add.legend=FALSE, standardize=FALSE,
                   col=NULL, main, ...)

Arguments

x	FeatureSet object
which	integer indices of samples to be plotted (optional).
transfo	function to be applied to the data prior to plotting.
type	Type of statistics to be used.
use.log	Use log.
add.legend	Add legend.
standardize	Standardize residuals.
col	Colors to be used.
main	Main title.
...	parameters to be passed to image

Examples

if(require(oligoData) & require(pd.hg18.60mer.expr)){
  data(nimbleExpressionFS)
  par(mfrow=c(1, 2))
  image(nimbleExpressionFS, which=4)
##  fit <- fitPLM(nimbleExpressionFS)
##  image(fit, which=4)
  plot(1) ## while fixing fitPLM TODO
}

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: oligoClasses
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
Welcome to oligoClasses version 1.38.0
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")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

================================================================================
Welcome to oligo version 1.40.2
================================================================================
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Loading required package: oligoData
Loading required package: pd.hg18.60mer.expr
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'oligoData'
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pd.hg18.60mer.expr'

oligo documentation built on Nov. 8, 2020, 6:52 p.m.