Example dataset for meta-analysis of microarray

Description

This is an example dataset for meta-analysis of microarray. It has been created from three datasets form Gene Expression Omnibus (GSE13067, GSE13294 and GSE4554). The data have been normalized, log2-transformed and only random selection of 500 gene is included.

Usage

data(ColonData)

Format

The format is: Formal class 'MetaArray' [package "MAMA"] with 3 slots ..@ GEDM :List of 3 .. ..$ : num [1:500, 1:77] 2.49 3.87 2.95 6.39 6.06 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:500] "217562_at" "203766_s_at" "1554394_at" "212662_at" ... .. .. .. ..$ : chr [1:77] "GSM335574" "GSM335645" "GSM335546" "GSM335623" ... .. ..$ : num [1:500, 1:36] 3.24 5.32 3.24 7.24 4.75 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:500] "217562_at" "203766_s_at" "1554394_at" "212662_at" ... .. .. .. ..$ : chr [1:36] "GSM327331" "GSM327282" "GSM327313" "GSM327353" ... .. ..$ : num [1:500, 1:41] 0.595 3 1.618 4.668 2.887 ... .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. ..$ : chr [1:500] "217562_at" "203766_s_at" "1554394_at" "212662_at" ... .. .. .. ..$ : chr [1:41] "GSM101849" "GSM101851" "GSM101857" "GSM101799" ... ..@ clinical :List of 3 .. ..$ :'data.frame': 77 obs. of 1 variable: .. .. ..$ satelite: Factor w/ 2 levels "MSI","MSS": 1 1 1 1 1 1 1 1 1 1 ... .. ..$ :'data.frame': 36 obs. of 1 variable: .. .. ..$ satelite: Factor w/ 2 levels "MSI","MSS": 1 1 1 1 1 2 2 2 2 2 ... .. ..$ :'data.frame': 41 obs. of 2 variables: .. .. ..$ position: Factor w/ 3 levels "distal","proximal",..: 2 1 2 2 1 3 2 2 1 2 ... .. .. ..$ satelite: Factor w/ 2 levels "MSI","MSS": 1 1 1 1 1 1 1 1 1 1 ... ..@ datanames: chr [1:3] "denmark" "australia" "japan"

Source

http://www.ncbi.nlm.nih.gov/geo/

Examples

data(ColonData)
plot(ColonData)

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(MAMA)
Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

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

    rowVars

Loading required package: xtable
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")'.

Loading required package: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

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

    multExpFDR, zScoreFDR, zScorePermuted, zScores

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MAMA/ColonData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ColonData
> ### Title: Example dataset for meta-analysis of microarray
> ### Aliases: ColonData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ColonData)
> plot(ColonData)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>