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.
Value
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.
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
curatedBreastDataExprSetList <- getCuratedBreastDataExprSetList(test = TRUE)
# what are all the names of the studies?
names(curatedBreastDataExprSetList)
#> [1] "study_1379_GPL1223_all" "study_2034_GPL96_all"
# what is the dimension of the gene expression matrix for study GSE2034?
dim(exprs(curatedBreastDataExprSetList$study_2034_GPL96_all))
#> [1] 500 30