Contents

1 Normalized expression data from GSE13015

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, 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
dat = ExperimentHub()
## snapshotDate(): 2021-11-15
hub = query(dat , "GSE13015")
temp = hub[["EH5429"]]
## see ?GSE13015 and browseVignettes('GSE13015') for documentation
## loading from cache
## require("SummarizedExperiment")

2 sessionInfo()

sessionInfo()
## R Under development (unstable) (2021-11-16 r81199)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.15-data-experiment/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-data-experiment/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] SummarizedExperiment_1.25.2 GenomicRanges_1.47.5       
##  [3] GenomeInfoDb_1.31.1         IRanges_2.29.1             
##  [5] S4Vectors_0.33.4            MatrixGenerics_1.7.0       
##  [7] matrixStats_0.61.0          GSE13015_1.3.0             
##  [9] GEOquery_2.63.1             Biobase_2.55.0             
## [11] ExperimentHub_2.3.4         AnnotationHub_3.3.6        
## [13] BiocFileCache_2.3.0         dbplyr_2.1.1               
## [15] BiocGenerics_0.41.2         BiocStyle_2.23.0           
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.2                    sass_0.4.0                   
##  [3] tidyr_1.1.4                   bit64_4.0.5                  
##  [5] jsonlite_1.7.2                bslib_0.3.1                  
##  [7] shiny_1.7.1                   assertthat_0.2.1             
##  [9] interactiveDisplayBase_1.33.0 BiocManager_1.30.16          
## [11] blob_1.2.2                    GenomeInfoDbData_1.2.7       
## [13] yaml_2.2.1                    BiocVersion_3.15.0           
## [15] lattice_0.20-45               pillar_1.6.4                 
## [17] RSQLite_2.2.8                 glue_1.5.0                   
## [19] limma_3.51.0                  digest_0.6.28                
## [21] promises_1.2.0.1              XVector_0.35.0               
## [23] Matrix_1.3-4                  preprocessCore_1.57.0        
## [25] htmltools_0.5.2               httpuv_1.6.3                 
## [27] pkgconfig_2.0.3               bookdown_0.24                
## [29] zlibbioc_1.41.0               purrr_0.3.4                  
## [31] xtable_1.8-4                  later_1.3.0                  
## [33] tzdb_0.2.0                    tibble_3.1.6                 
## [35] KEGGREST_1.35.0               generics_0.1.1               
## [37] ellipsis_0.3.2                cachem_1.0.6                 
## [39] withr_2.4.2                   magrittr_2.0.1               
## [41] crayon_1.4.2                  mime_0.12                    
## [43] memoise_2.0.0                 evaluate_0.14                
## [45] fansi_0.5.0                   xml2_1.3.2                   
## [47] tools_4.2.0                   data.table_1.14.2            
## [49] hms_1.1.1                     lifecycle_1.0.1              
## [51] stringr_1.4.0                 DelayedArray_0.21.2          
## [53] AnnotationDbi_1.57.1          Biostrings_2.63.0            
## [55] compiler_4.2.0                jquerylib_0.1.4              
## [57] rlang_0.4.12                  grid_4.2.0                   
## [59] RCurl_1.98-1.5                rappdirs_0.3.3               
## [61] bitops_1.0-7                  rmarkdown_2.11               
## [63] DBI_1.1.1                     curl_4.3.2                   
## [65] R6_2.5.1                      knitr_1.36                   
## [67] dplyr_1.0.7                   fastmap_1.1.0                
## [69] bit_4.0.4                     utf8_1.2.2                   
## [71] filelock_1.0.2                readr_2.1.0                  
## [73] stringi_1.7.5                 Rcpp_1.0.7                   
## [75] vctrs_0.3.8                   png_0.1-7                    
## [77] tidyselect_1.1.1              xfun_0.28