Colorectal array CGH dataset

Description

The colorectal dataset is an object of class aCGH. It represents a collection of 124 array CGH profiles of primary colorectal tumors and their derived attributes. Each sample was measured on the BAC clone DNA microarray with approximate resolution of 1.4 Mb per clone. There were approximately 2400 clones spotted on the array and each clone was printed in triplicates located immediately next to each other. Each array consisted of the 16 (4 by 4) subarrays. The clones were mapped on the July 03 UCSC freeze. There were a number of the discrete and continious phenotypes associated with the samples such as age, mutation status for various markers, stage, location and so on. All images were quantified and normalized by Dr. Taku Tokuyasu using custom image software SPOT and postprocessing custom software SPROC.

Usage

data(colorectal)

Source

These data were generated at Dr. Fred Waldman's lab at UCSF Cancer Center by K. Nakao and K. Mehta. The manuscript describing the data and the analysis are described in High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization, Carcinogenesis, 2004, Nakao et. al.

References

Nakao et. al., High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization, Carcinogenesis, 2004 Jain et. al, Fully automatic quantification of microarray image data, Genome Research, 2003

See Also

aCGH plotGenome

Examples

data(colorectal)
## WARNING: plotting the heatmap takes some time
plot(colorectal)
plotGenome(colorectal[,1:2])

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(aCGH)
Loading required package: cluster
Loading required package: survival
Loading required package: multtest
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")'.


Attaching package: 'aCGH'

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

    heatmap

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/aCGH/colorectal.Rd_%03d_medium.png", width=480, height=480)
> ### Name: colorectal
> ### Title: Colorectal array CGH dataset
> ### Aliases: colorectal clones.info.ex log2.ratios.ex pheno.type.ex
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(colorectal)
> ## WARNING: plotting the heatmap takes some time
> plot(colorectal)
> plotGenome(colorectal[,1:2])
Warning message:
In `[.aCGH`(colorectal, , 1:2) : subsetting the log2.ratios only
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>