Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession GSE13015. GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub can be used for Differential Expression Analysis, Modular repertiore analysis.
In the below example, we show how one can download this dataset from ExperimentHub.
## Loading required package: BiocGenerics## Loading required package: generics##
## Attaching package: 'generics'## The following objects are masked from 'package:base':
##
## as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
## setequal, union##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
##
## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique,
## unsplit, which.max, which.min## Loading required package: AnnotationHub## Loading required package: BiocFileCache## Loading required package: dbplyr## Setting options('download.file.method.GEOquery'='auto')## Setting options('GEOquery.inmemory.gpl'=FALSE)## see ?GSE13015 and browseVignettes('GSE13015') for documentation## downloading 1 resources## retrieving 1 resource## loading from cache## require("SummarizedExperiment")## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] SummarizedExperiment_1.42.0 GenomicRanges_1.64.0
## [3] Seqinfo_1.2.0 IRanges_2.46.0
## [5] S4Vectors_0.50.3 MatrixGenerics_1.24.0
## [7] matrixStats_1.5.0 GSE13015_1.20.0
## [9] GEOquery_2.80.0 Biobase_2.72.0
## [11] ExperimentHub_3.2.2 AnnotationHub_4.2.2
## [13] BiocFileCache_3.2.0 dbplyr_2.6.0
## [15] BiocGenerics_0.58.1 generics_0.1.4
## [17] BiocStyle_2.40.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.52.2 xfun_0.61 bslib_0.12.0
## [4] httr2_1.3.0 lattice_0.23-1 tzdb_0.5.0
## [7] vctrs_0.7.3 tools_4.6.1 curl_8.0.0
## [10] tibble_3.3.1 AnnotationDbi_1.74.0 RSQLite_3.53.3
## [13] blob_1.3.0 pkgconfig_2.0.3 Matrix_1.7-6
## [16] data.table_1.18.6.1 rentrez_1.2.4 lifecycle_1.0.5
## [19] compiler_4.6.1 Biostrings_2.80.2 statmod_1.5.2
## [22] htmltools_0.5.9 sys_3.4.3 buildtools_1.0.0
## [25] sass_0.4.10 yaml_2.3.12 preprocessCore_1.74.0
## [28] tidyr_1.3.2 pillar_1.11.1 crayon_1.5.3
## [31] jquerylib_0.1.4 limma_3.68.5 DelayedArray_0.38.2
## [34] cachem_1.1.0 abind_1.4-8 tidyselect_1.2.1
## [37] digest_0.6.39 dplyr_1.2.1 purrr_1.2.2
## [40] BiocVersion_3.23.1 maketools_1.3.2 grid_4.6.1
## [43] fastmap_1.2.0 SparseArray_1.12.3 cli_3.6.6
## [46] magrittr_2.0.5 S4Arrays_1.12.1 XML_3.99-0.25
## [49] readr_2.2.0 withr_3.0.3 filelock_1.0.3
## [52] rappdirs_0.3.4 bit64_4.8.6 rmarkdown_2.32
## [55] XVector_0.52.0 httr_1.4.9 bit_4.6.0
## [58] hms_1.1.4 png_0.1-9 memoise_2.0.1
## [61] evaluate_1.0.5 knitr_1.52 rlang_1.3.0
## [64] glue_1.8.1 DBI_1.3.0 xml2_1.6.0
## [67] BiocManager_1.30.27 jsonlite_2.0.0 R6_2.6.1