R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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
>