Last data update: 2014.03.03

R: Cross-hybridisation simulation
runSimulationR Documentation

Cross-hybridisation simulation

Description

Cross-hybridisation simulation

Usage

  runSimulation()

Format

runSimulation is a function that will run the simulation we ran for our study. By modifying the parameters, users can play with it themselves.

Author(s)

Tineke Casneuf tine@ebi.ac.uk

References

Casneuf, Van de Peer and Huber (Submitted).

Examples

  runSimulation()

## see also the vignette

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 '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(XhybCasneuf)
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")'.

Loading required package: ath1121501cdf

Loading required package: tinesath1cdf

Attaching package: 'tinesath1cdf'

The following objects are masked from 'package:ath1121501cdf':

    i2xy, xy2i

Loading required package: RColorBrewer
Loading required package: grid
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'ath1121501cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'ath1121501cdf' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XhybCasneuf/runSimulation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: runSimulation
> ### Title: Cross-hybridisation simulation
> ### Aliases: runSimulation
> ### Keywords: manip
> 
> ### ** Examples
> 
>   runSimulation()
Plot background-corrected, normalised expression data of reporters:  
   - of probe set  A  -> plot  A 
   - of probe set  B  -> plot  B 
   - of probe set  C  -> plot  C 
Plot median-polish summarised expression data of the three probe sets -> plot D


***  Pearson correlation coefficients between expression values summarised with:
*** median polish ***
corr.: probe sets A and B:  -0.0692 
corr.: probe sets A and C:  0.731 

*** tuckey's biweight ***
corr.: probe sets A and B:  -0.223 
corr.: probe sets A and C:  -0.19 

*** dChip ***
corr.: probe sets A and B:  0.296 
corr.: probe sets A and C:  0.947 

> 
> ## see also the vignette
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>