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##
## 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, intersect, is.unsorted,
## lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: AnnotationHub## Loading required package: BiocFileCache## Loading required package: dbplyr## Warning: replacing previous import 'utils::findMatches' by
## 'S4Vectors::findMatches' when loading 'AnnotationDbi'dat = ExperimentHub()
hub = query(dat , "GSE13015")
temp = hub[["EH5429"]]## see ?GSE13015 and browseVignettes('GSE13015') for documentation## loading from cache## require("SummarizedExperiment")sessionInfo()## R version 4.3.0 RC (2023-04-13 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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_1.30.0 GenomicRanges_1.52.0
## [3] GenomeInfoDb_1.36.0 IRanges_2.34.0
## [5] S4Vectors_0.38.0 MatrixGenerics_1.12.0
## [7] matrixStats_0.63.0 GSE13015_1.8.0
## [9] GEOquery_2.68.0 Biobase_2.60.0
## [11] ExperimentHub_2.8.0 AnnotationHub_3.8.0
## [13] BiocFileCache_2.8.0 dbplyr_2.3.2
## [15] BiocGenerics_0.46.0 BiocStyle_2.28.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.0 dplyr_1.1.2
## [3] blob_1.2.4 filelock_1.0.2
## [5] Biostrings_2.68.0 bitops_1.0-7
## [7] fastmap_1.1.1 RCurl_1.98-1.12
## [9] promises_1.2.0.1 digest_0.6.31
## [11] mime_0.12 lifecycle_1.0.3
## [13] ellipsis_0.3.2 KEGGREST_1.40.0
## [15] interactiveDisplayBase_1.38.0 RSQLite_2.3.1
## [17] magrittr_2.0.3 compiler_4.3.0
## [19] rlang_1.1.0 sass_0.4.5
## [21] tools_4.3.0 utf8_1.2.3
## [23] yaml_2.3.7 data.table_1.14.8
## [25] knitr_1.42 bit_4.0.5
## [27] curl_5.0.0 DelayedArray_0.26.0
## [29] xml2_1.3.3 withr_2.5.0
## [31] purrr_1.0.1 grid_4.3.0
## [33] preprocessCore_1.62.0 fansi_1.0.4
## [35] xtable_1.8-4 cli_3.6.1
## [37] rmarkdown_2.21 crayon_1.5.2
## [39] generics_0.1.3 httr_1.4.5
## [41] tzdb_0.3.0 DBI_1.1.3
## [43] cachem_1.0.7 zlibbioc_1.46.0
## [45] AnnotationDbi_1.62.0 BiocManager_1.30.20
## [47] XVector_0.40.0 vctrs_0.6.2
## [49] Matrix_1.5-4 jsonlite_1.8.4
## [51] bookdown_0.33 hms_1.1.3
## [53] bit64_4.0.5 limma_3.56.0
## [55] jquerylib_0.1.4 tidyr_1.3.0
## [57] glue_1.6.2 BiocVersion_3.17.1
## [59] later_1.3.0 tibble_3.2.1
## [61] pillar_1.9.0 rappdirs_0.3.3
## [63] htmltools_0.5.5 GenomeInfoDbData_1.2.10
## [65] R6_2.5.1 lattice_0.21-8
## [67] evaluate_0.20 shiny_1.7.4
## [69] readr_2.1.4 png_0.1-8
## [71] memoise_2.0.1 httpuv_1.6.9
## [73] bslib_0.4.2 Rcpp_1.0.10
## [75] xfun_0.39 pkgconfig_2.0.3