Downloads GSE20685 (Li *et al.*, 2010) from GEO via
GEOquery::getGEO() (which caches the series matrix itself),
performs probe-to-gene collapse (largest mean expression per symbol),
subsets to the top 3000 most variable genes, and returns a
SummarizedExperiment with an exprs assay (microarray log2
intensities, used as-is by the pipeline) and clinical metadata
(time, event, age, subtype).
fetch_gse20685()A SummarizedExperiment or NULL if the download or
processing fails (e.g. network unavailable, GEOquery not
installed).
This helper packages the processing pipeline from
inst/scripts/repro_gse20685.R for use in vignettes. The full
series matrix is downloaded from GEO, probes are collapsed to gene symbols
by largest mean expression, and the top 3000 most variable genes are
retained. Clinical metadata includes overall-survival follow-up time
(years), event indicator (1 = death), age at diagnosis, and breast-cancer
subtype.
# \donttest{
se <- fetch_gse20685()
#> Downloading GSE20685 from GEO ...
#> Found 1 file(s)
#> GSE20685_series_matrix.txt.gz
se
#> class: SummarizedExperiment
#> dim: 3000 327
#> metadata(0):
#> assays(1): exprs
#> rownames(3000): CRISP3 S100A7 ... HYDIN MAGEB3
#> rowData names(0):
#> colnames(327): GSM519117 GSM519118 ... GSM519442 GSM519443
#> colData names(4): time event age subtype
# }