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: dbplyrdat = 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 Under development (unstable) (2025-10-20 r88955)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.23-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_1.39.2 GenomicRanges_1.61.6
## [3] Seqinfo_0.99.3 IRanges_2.43.5
## [5] S4Vectors_0.47.4 MatrixGenerics_1.21.0
## [7] matrixStats_1.5.0 GSE13015_1.17.0
## [9] GEOquery_2.77.6 Biobase_2.69.1
## [11] ExperimentHub_2.99.6 AnnotationHub_3.99.6
## [13] BiocFileCache_2.99.6 dbplyr_2.5.1
## [15] BiocGenerics_0.55.4 generics_0.1.4
## [17] BiocStyle_2.37.1
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.49.2 xfun_0.53 bslib_0.9.0
## [4] httr2_1.2.1 lattice_0.22-7 tzdb_0.5.0
## [7] vctrs_0.6.5 tools_4.6.0 curl_7.0.0
## [10] tibble_3.3.0 AnnotationDbi_1.71.2 RSQLite_2.4.3
## [13] blob_1.2.4 pkgconfig_2.0.3 Matrix_1.7-4
## [16] data.table_1.17.8 rentrez_1.2.4 lifecycle_1.0.4
## [19] compiler_4.6.0 Biostrings_2.77.2 statmod_1.5.1
## [22] htmltools_0.5.8.1 sass_0.4.10 yaml_2.3.10
## [25] preprocessCore_1.71.2 tidyr_1.3.1 pillar_1.11.1
## [28] crayon_1.5.3 jquerylib_0.1.4 limma_3.65.7
## [31] DelayedArray_0.35.3 cachem_1.1.0 abind_1.4-8
## [34] tidyselect_1.2.1 digest_0.6.37 dplyr_1.1.4
## [37] purrr_1.1.0 bookdown_0.45 BiocVersion_3.22.0
## [40] grid_4.6.0 fastmap_1.2.0 SparseArray_1.9.1
## [43] cli_3.6.5 magrittr_2.0.4 S4Arrays_1.9.1
## [46] XML_3.99-0.19 readr_2.1.5 withr_3.0.2
## [49] filelock_1.0.3 rappdirs_0.3.3 bit64_4.6.0-1
## [52] rmarkdown_2.30 XVector_0.49.1 httr_1.4.7
## [55] bit_4.6.0 hms_1.1.4 png_0.1-8
## [58] memoise_2.0.1 evaluate_1.0.5 knitr_1.50
## [61] rlang_1.1.6 glue_1.8.0 DBI_1.2.3
## [64] xml2_1.4.0 BiocManager_1.30.26 jsonlite_2.0.0
## [67] R6_2.6.1