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.
library(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':
##
## Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
## as.data.frame, basename, cbind, colnames, dirname, do.call,
## duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
## mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
## unsplit, which.max, which.min## Loading required package: AnnotationHub## Loading required package: BiocFileCache## Loading required package: dbplyr## Registered S3 method overwritten by 'bit64':
## method from
## print.bitstring toolsdat = ExperimentHub()
hub = query(dat , "GSE13015")
temp = hub[["EH5429"]]## Setting options('download.file.method.GEOquery'='auto')## Setting options('GEOquery.inmemory.gpl'=FALSE)## see ?GSE13015 and browseVignettes('GSE13015') for documentation## loading from cache## require("SummarizedExperiment")sessionInfo()## R version 4.6.0 RC (2026-04-17 r89917)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [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: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] SummarizedExperiment_1.41.1 GenomicRanges_1.63.2
## [3] Seqinfo_1.1.0 IRanges_2.45.0
## [5] S4Vectors_0.49.2 MatrixGenerics_1.23.0
## [7] matrixStats_1.5.0 GSE13015_1.19.0
## [9] GEOquery_2.79.0 Biobase_2.71.0
## [11] ExperimentHub_3.1.0 AnnotationHub_4.1.0
## [13] BiocFileCache_3.1.0 dbplyr_2.5.2
## [15] BiocGenerics_0.57.1 generics_0.1.4
## [17] BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.51.1 xfun_0.57 bslib_0.10.0
## [4] httr2_1.2.2 lattice_0.22-9 tzdb_0.5.0
## [7] vctrs_0.7.3 tools_4.6.0 curl_7.0.0
## [10] tibble_3.3.1 AnnotationDbi_1.73.1 RSQLite_2.4.6
## [13] blob_1.3.0 pkgconfig_2.0.3 Matrix_1.7-5
## [16] data.table_1.18.2.1 rentrez_1.2.4 lifecycle_1.0.5
## [19] compiler_4.6.0 Biostrings_2.79.5 statmod_1.5.1
## [22] htmltools_0.5.9 sass_0.4.10 yaml_2.3.12
## [25] preprocessCore_1.73.0 tidyr_1.3.2 pillar_1.11.1
## [28] crayon_1.5.3 jquerylib_0.1.4 limma_3.67.1
## [31] DelayedArray_0.37.1 cachem_1.1.0 abind_1.4-8
## [34] tidyselect_1.2.1 digest_0.6.39 dplyr_1.2.1
## [37] purrr_1.2.2 bookdown_0.46 BiocVersion_3.23.1
## [40] grid_4.6.0 fastmap_1.2.0 SparseArray_1.11.13
## [43] cli_3.6.6 magrittr_2.0.5 S4Arrays_1.11.1
## [46] XML_3.99-0.23 readr_2.2.0 withr_3.0.2
## [49] filelock_1.0.3 rappdirs_0.3.4 bit64_4.6.0-1
## [52] rmarkdown_2.31 XVector_0.51.0 httr_1.4.8
## [55] bit_4.6.0 otel_0.2.0 hms_1.1.4
## [58] png_0.1-9 memoise_2.0.1 evaluate_1.0.5
## [61] knitr_1.51 rlang_1.2.0 glue_1.8.1
## [64] DBI_1.3.0 xml2_1.5.2 BiocManager_1.30.27
## [67] jsonlite_2.0.0 R6_2.6.1