plotILM

Description

Illustrate the Langmuir Isotherm for selected probe set.

Usage

plotILM(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. Optional plot.error argument (numeric) can be used to define the illustration of the variability. plot.error=1 computes the error on the log scale. plot.error=2 (default value) computes the error on the concentrations. plot.error=3 computes the error on the concentrations, for 2 intervals. Note that error curves can only be plotted if concentration is higher than error (negative concentration does not exist!).

Author(s)

Myriam Kroll, Fabrice Berger and Enrico Carlon

See Also

ILM,plotIntens

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
plotILM(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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/plotILM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotILM
> ### Title: plotILM
> ### Aliases: plotILM plotILM,ILM-method plotILM,ILM,character-method
> ###   plotILM,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
> plotILM(result2,y="203561_at",z="HG-Focus-2-121502.CEL")
Median =  19 
M.a.d. =  22.28 
$Ipm
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
          147.5           418.8           128.0            77.0            77.3 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
           91.0           147.5           103.0           139.3            91.5 
ps.203561_at.id 
           66.5 

$I0pm
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
              0               0               0               0               0 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
              0               0               0               0               0 
ps.203561_at.id 
              0 

$ImI0
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
          147.5           418.8           128.0            77.0            77.3 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
           91.0           147.5           103.0           139.3            91.5 
ps.203561_at.id 
           66.5 

$deltaG
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
       39.10055        33.29936        28.36574        32.71198        26.90984 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
       28.43224        31.45188        31.89483        33.77644        28.47270 
ps.203561_at.id 
       26.68979 

$deltaGp
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
       60.14510        52.17196        45.73236        52.74425        47.35857 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
       44.22202        46.73415        53.49765        53.11425        47.04423 
ps.203561_at.id 
       46.34745 

$alpha
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
   8.604633e-05    2.001674e-02    6.286903e-01    1.360587e-02    3.568698e-01 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
   8.267394e-01    4.599292e-01    8.159426e-03    1.058815e-02    4.077343e-01 
ps.203561_at.id 
   5.261385e-01 

$deltaGpRTlogA
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
       26.45106        28.01397        27.73856        26.90488        25.51743 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
       28.17512        30.40230        25.39675        27.63047        27.26035 
ps.203561_at.id 
       25.82197 

$Concs
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
      47.256391       43.402603       15.785002       17.507097       49.069528 
ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id ps.203561_at.id 
       8.093745        2.538730       71.676878       18.630330       16.015396 
ps.203561_at.id 
      33.659571 

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> dev.off()
null device 
          1 
>