Subset Microarray Data from St.Jude Children Research Hospital (USA)

Description

Example for list-structure used by many functions in MACAT. It's based on the gene expression data published by Yeoh et al. (2002) The data has been preprocessed using 'vsn' on probe level and the probe values have been summed up to probe set values using the 'median polish' procedure. This is a subset of the data, containing only the data for the 5000 probe sets with the highest variance across the samples and for 10 exemplary samples, 5 from T-lymphocytic Acute Lymphocytic Leukemia (ALL) and 5 from B-lymphocytic ALL.

Usage

data(stjd)

Format

List of class 'MACATData' with 6 components:

geneName:

Identifiers of genes/probe sets in expression data

geneLocation:

Location of genes on their chromosome as distance from 5'end in base pairs Negative numbers denote genes on the antisense strand.

chromosome:

Chromosome of the respective gene. Components 'geneName', 'geneLocation', and 'chromosome' are in the same order.

expr:

expression matrix with rows = genes and columns = samples/patients

labels:

(disease) subtype of each sample, has length = number of columns of expression matrix

chip:

Identifier for Microarray used for the experiments (here for the Affymetrix HG-U95av2 Oligonucleotide GeneChip)

Note

For the full data package see the Bioconductor data package stjudem. If it is not already installed on your system, try source("http:www.bioconductor.orgiocLite.R"); biocLite("stjudem")

References

Yeoh et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell. March 2002. 1: 133-143.

See Also

buildMACAT,stjude in package 'stjudem' for the complete expression data

Examples

data(stjd)
summary(stjd)

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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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(macat)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
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

Loading required package: XML
Loading MicroArray Chromosome Analysis Tool...
Loading required packages...

Type 'demo(macatdemo)' for a quick tour...

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/macat/stjd.Rd_%03d_medium.png", width=480, height=480)
> ### Name: stjd
> ### Title: Subset Microarray Data from St.Jude Children Research Hospital
> ###   (USA)
> ### Aliases: stjd
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(stjd)
> summary(stjd)
             Length Class  Mode     
geneName      5208  -none- character
geneLocation  5208  -none- numeric  
chromosome    5208  -none- character
expr         50000  -none- numeric  
labels          10  -none- character
chip             1  -none- character
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>