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"]]## see ?GSE13015 and browseVignettes('GSE13015') for documentation## loading from cache## require("SummarizedExperiment")sessionInfo()## R version 4.5.0 RC (2025-04-04 r88126)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-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_1.38.0 GenomicRanges_1.60.0
## [3] GenomeInfoDb_1.44.0 IRanges_2.42.0
## [5] S4Vectors_0.46.0 MatrixGenerics_1.20.0
## [7] matrixStats_1.5.0 GSE13015_1.16.0
## [9] GEOquery_2.76.0 Biobase_2.68.0
## [11] ExperimentHub_2.16.0 AnnotationHub_3.16.0
## [13] BiocFileCache_2.16.0 dbplyr_2.5.0
## [15] BiocGenerics_0.54.0 generics_0.1.3
## [17] BiocStyle_2.36.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 dplyr_1.1.4 blob_1.2.4
## [4] filelock_1.0.3 Biostrings_2.76.0 fastmap_1.2.0
## [7] XML_3.99-0.18 digest_0.6.37 mime_0.13
## [10] lifecycle_1.0.4 statmod_1.5.0 KEGGREST_1.48.0
## [13] RSQLite_2.3.9 magrittr_2.0.3 compiler_4.5.0
## [16] rlang_1.1.6 sass_0.4.10 tools_4.5.0
## [19] yaml_2.3.10 data.table_1.17.0 knitr_1.50
## [22] S4Arrays_1.8.0 bit_4.6.0 curl_6.2.2
## [25] DelayedArray_0.34.0 xml2_1.3.8 abind_1.4-8
## [28] withr_3.0.2 purrr_1.0.4 grid_4.5.0
## [31] preprocessCore_1.70.0 cli_3.6.4 rmarkdown_2.29
## [34] crayon_1.5.3 httr_1.4.7 tzdb_0.5.0
## [37] DBI_1.2.3 cachem_1.1.0 AnnotationDbi_1.70.0
## [40] BiocManager_1.30.25 XVector_0.48.0 vctrs_0.6.5
## [43] Matrix_1.7-3 jsonlite_2.0.0 bookdown_0.43
## [46] hms_1.1.3 bit64_4.6.0-1 limma_3.64.0
## [49] jquerylib_0.1.4 tidyr_1.3.1 glue_1.8.0
## [52] BiocVersion_3.21.1 UCSC.utils_1.4.0 tibble_3.2.1
## [55] pillar_1.10.2 rappdirs_0.3.3 htmltools_0.5.8.1
## [58] GenomeInfoDbData_1.2.14 R6_2.6.1 evaluate_1.0.3
## [61] lattice_0.22-7 readr_2.1.5 rentrez_1.2.3
## [64] png_0.1-8 memoise_2.0.1 bslib_0.9.0
## [67] SparseArray_1.8.0 xfun_0.52 pkgconfig_2.0.3