curatedBreastDataExprSetList

Description

A list of ExpressionSet objects, one for each curated study, containing study-specific gene expression and phenotype data. FeatureNames are gene symbols. Data is already quantile normalized according to standard protocols for 1 and 2-channel arrays, depending on the platform used for this study.

Usage

data("curatedBreastDataExprSetList")

Format

A list, with each index containing an ExpressionSet object from a specific study, and potentially a specific batch.

Details

Batches from studies are treated as individual datasets, as the signal can differ between batches. Thus, an expression object named using a GSE study number followed by an underscore means this ExpressionSet contains samples either from a distinct platform (and the study used >1 platforms), or from a distinct batch or tissue site. An "all" tag means that there were no batches for this study. Raw data files downloaded from GEO oftentimes have clear batch/site information appended to sample names; this was often the source of batch identification and how the package developer chose to create the batch name string.

Value

No return value as this is not a function but rather a data object.

References

Planey, Butte. Database integration of 4923 publicly-available samples of breast cancer molecular and clinical data. AMIA Joint Summits Translational Science Proceedings. (2003) PMC3814460

Examples

data(curatedBreastDataExprSetList)
#what are all the names of the studies?
names(curatedBreastDataExprSetList)
#what is the dimension of the gene 
#expression matrix for study GSE17705 from the JBI 
#(as opposed to MDACC) site?
dim(exprs(curatedBreastDataExprSetList$study_17705_GPL96_JBI_Tissue_BC_Tamoxifen))

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(curatedBreastData)
Loading required package: ggplot2
Loading required package: impute
Loading required package: XML
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: BiocStyle
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/curatedBreastData/curatedBreastDataExprSetList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: curatedBreastDataExprSetList
> ### Title: curatedBreastDataExprSetList
> ### Aliases: curatedBreastDataExprSetList
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(curatedBreastDataExprSetList)
> #what are all the names of the studies?
> names(curatedBreastDataExprSetList)
 [1] "study_1379_GPL1223_all"                     
 [2] "study_2034_GPL96_all"                       
 [3] "study_4913_GPL3558_all"                     
 [4] "study_6577_GPL3883_all"                     
 [5] "study_9893_GPL5049_all"                     
 [6] "study_12071_GPL5186_all"                    
 [7] "study_12093_GPL96_all"                      
 [8] "study_16391_GPL570_all"                     
 [9] "study_16446_GPL570_all"                     
[10] "study_17705_GPL96_JBI_Tissue_BC_Tamoxifen"  
[11] "study_17705_GPL96_MDACC_Tissue_BC_Tamoxifen"
[12] "study_18728_GPL570_all"                     
[13] "study_19615_GPL570_all"                     
[14] "study_19697_GPL570_all"                     
[15] "study_20181_GPL96_all"                      
[16] "study_20194_GPL96_all"                      
[17] "study_21974_GPL6480_all"                    
[18] "study_21997_GPL1390_all"                    
[19] "study_21997_GPL5325_all"                    
[20] "study_21997_GPL7504_all"                    
[21] "study_22226_GPL1708_all"                    
[22] "study_22226_GPL4133_all"                    
[23] "study_22358_GPL5325_all"                    
[24] "study_23428_GPL5325_all"                    
[25] "study_25055_GPL96_MDACC_M"                  
[26] "study_25055_GPL96_MDACC_PERU"               
[27] "study_25065_GPL96_LBJ"                      
[28] "study_25065_GPL96_MDACC"                    
[29] "study_25065_GPL96_MDACC_MDA"                
[30] "study_25065_GPL96_PERU"                     
[31] "study_25065_GPL96_Spain"                    
[32] "study_25065_GPL96_USO"                      
[33] "study_32646_GPL570_all"                     
[34] "study_33658_GPL570_all"                     
> #what is the dimension of the gene 
> #expression matrix for study GSE17705 from the JBI 
> #(as opposed to MDACC) site?
> dim(exprs(curatedBreastDataExprSetList$study_17705_GPL96_JBI_Tissue_BC_Tamoxifen))
[1] 22293   103
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>