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 object is masked from 'package:utils':
##
## data## 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, scale, sequence, table,
## tapply, transform, 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_1.43.0 GenomicRanges_1.65.4
## [3] Seqinfo_1.3.2 IRanges_2.47.5
## [5] S4Vectors_0.51.10 MatrixGenerics_1.25.0
## [7] matrixStats_1.5.0 GSE13015_1.21.0
## [9] GEOquery_2.81.28 Biobase_2.73.2
## [11] ExperimentHub_3.3.2 AnnotationHub_4.3.2
## [13] BiocFileCache_3.3.0 dbplyr_2.6.0
## [15] BiocGenerics_0.59.12 generics_0.1.4
## [17] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.53.6 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_1.75.2 RSQLite_3.53.3
## [13] blob_1.3.0 pkgconfig_2.0.3 BiocBaseUtils_1.15.1
## [16] Matrix_1.7-6 data.table_1.18.6.1 rentrez_1.2.4
## [19] lifecycle_1.0.5 compiler_4.6.1 Biostrings_2.81.9
## [22] statmod_1.5.2 htmltools_0.5.9 sys_3.4.3
## [25] buildtools_1.0.0 sass_0.4.10 yaml_2.3.12
## [28] preprocessCore_1.75.1 tidyr_1.3.2 pillar_1.11.1
## [31] crayon_1.5.3 jquerylib_0.1.4 limma_3.99.0
## [34] DelayedArray_0.39.8 cachem_1.1.0 abind_1.4-8
## [37] tidyselect_1.2.1 digest_0.6.39 dplyr_1.2.1
## [40] purrr_1.2.2 BiocVersion_3.24.0 maketools_1.3.2
## [43] grid_4.6.1 fastmap_1.2.0 SparseArray_1.13.4
## [46] cli_3.6.6 magrittr_2.0.5 S4Arrays_1.13.2
## [49] XML_3.99-0.25 readr_2.2.0 withr_3.0.3
## [52] filelock_1.0.3 rappdirs_0.3.4 bit64_4.8.6
## [55] rmarkdown_2.32 XVector_0.53.0 httr_1.4.9
## [58] bit_4.6.0 hms_1.1.4 png_0.1-9
## [61] memoise_2.0.1 evaluate_1.0.5 knitr_1.52
## [64] rlang_1.3.0 glue_1.8.1 DBI_1.3.0
## [67] xml2_1.6.0 BiocManager_1.30.27 jsonlite_2.0.0
## [70] R6_2.6.1