plotIntens

Description

Plot the PM intensity and the calculated background of one probe set.

Usage

plotIntens(object,y,z,...)

Arguments

Details

plotIntens plots one graph for each CEL-file. Note that it is only possible to plot one probe set at a time (if y (or z) is a vector, only the first value is used). If y=NULL or z=NULL, there is no output.

Author(s)

Myriam Kroll, Fabrice Berger and Enrico Carlon

See Also

ILM,plotILM

Examples

path <- system.file("rawData", "FusionSDK_HG-Focus", "HG-Focus", "2.Calvin",
    package="AffymetrixDataTestFiles")
file1 <- file.path(path,"HG-Focus-1-121502.CEL")
file2 <- file.path(path,"HG-Focus-2-121502.CEL")
result2 <- ilm(c(file1,file2))
## plot output
plotIntens(result2,y="203561_at",z="HG-Focus-2-121502.CEL")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(affyILM)
Loading required package: gcrma
Loading required package: affy
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

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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affyILM/plotIntens.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotIntens
> ### Title: plotIntens
> ### Aliases: plotIntens plotIntens,ILM-method
> ###   plotIntens,ILM,character-method plotIntens,ILM,missing-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> path <- system.file("rawData", "FusionSDK_HG-Focus", "HG-Focus", "2.Calvin",
+     package="AffymetrixDataTestFiles")
> file1 <- file.path(path,"HG-Focus-1-121502.CEL")
> file2 <- file.path(path,"HG-Focus-2-121502.CEL")
> result2 <- ilm(c(file1,file2))
Chip dimension 448  x  448 
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Probepackage hgfocusprobe loaded 
Reading intensities...[1] ...done
Computing hybridization free energies...
...done
Computing concentrations...
...done
Scaling concentrations between arrays...
Warning message:
In is.na(na.replace) :
  is.na() applied to non-(list or vector) of type 'NULL'
> ## plot output
> plotIntens(result2,y="203561_at",z="HG-Focus-2-121502.CEL")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>