This data set is from protein expression data captured for 39 proteins. It has two batches and two conditions corresponding to case and control.
This data set is from signature data captured when activating different growth pathway genes in human mammary epithelial cells (GEO accession: GSE73628). This data consists of three batches and ten different conditions corresponding to control and nine different pathways
This data set is from bladder cancer data. This dataset has 57 bladder samples with 5 batches and 3 covariate levels (cancer, biopsy, control). Batch 1 contains only cancer, 2 has cancer and controls, 3 has only controls, 4 contains only biopsy, and 5 contains cancer and biopsy. This data set is from the bladderbatch package which must be installed to use this data example set (Leek JT (2023). bladderbatch: Bladder gene expression data illustrating batch effects. R package version 1.38.0).
## R version 4.4.3 (2025-02-28)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BatchQC_2.3.5 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 ggdendro_0.2.0
## [3] sys_3.4.3 jsonlite_1.9.1
## [5] umap_0.2.10.0 magrittr_2.0.3
## [7] NCmisc_1.2.0 farver_2.1.2
## [9] rmarkdown_2.29 vctrs_0.6.5
## [11] memoise_2.0.1 EBSeq_2.5.2
## [13] askpass_1.2.1 htmltools_0.5.8.1
## [15] S4Arrays_1.7.3 BiocNeighbors_2.1.3
## [17] SparseArray_1.7.6 sass_0.4.9
## [19] KernSmooth_2.23-26 bslib_0.9.0
## [21] htmlwidgets_1.6.4 plyr_1.8.9
## [23] testthat_3.2.3 plotly_4.10.4
## [25] cachem_1.1.0 buildtools_1.0.0
## [27] igraph_2.1.4 mime_0.13
## [29] lifecycle_1.0.4 pkgconfig_2.0.3
## [31] rsvd_1.0.5 Matrix_1.7-3
## [33] R6_2.6.1 fastmap_1.2.0
## [35] GenomeInfoDbData_1.2.13 MatrixGenerics_1.19.1
## [37] shiny_1.10.0 digest_0.6.37
## [39] colorspace_2.1-1 ggnewscale_0.5.1
## [41] AnnotationDbi_1.69.0 S4Vectors_0.45.4
## [43] DESeq2_1.47.5 RSpectra_0.16-2
## [45] dqrng_0.4.1 irlba_2.3.5.1
## [47] crosstalk_1.2.1 GenomicRanges_1.59.1
## [49] RSQLite_2.3.9 beachmat_2.23.7
## [51] labeling_0.4.3 httr_1.4.7
## [53] abind_1.4-8 mgcv_1.9-1
## [55] compiler_4.4.3 withr_3.0.2
## [57] bit64_4.6.0-1 BiocParallel_1.41.2
## [59] DBI_1.2.3 gplots_3.2.0
## [61] MASS_7.3-65 openssl_2.3.2
## [63] DelayedArray_0.33.6 bluster_1.17.0
## [65] gtools_3.9.5 caTools_1.18.3
## [67] tools_4.4.3 httpuv_1.6.15
## [69] glue_1.8.0 nlme_3.1-167
## [71] promises_1.3.2 grid_4.4.3
## [73] cluster_2.1.8.1 reshape2_1.4.4
## [75] generics_0.1.3 sva_3.55.0
## [77] gtable_0.3.6 tidyr_1.3.1
## [79] data.table_1.17.0 utf8_1.2.4
## [81] BiocSingular_1.23.0 ScaledMatrix_1.15.0
## [83] metapod_1.15.0 XVector_0.47.2
## [85] BiocGenerics_0.53.6 pillar_1.10.1
## [87] stringr_1.5.1 limma_3.63.9
## [89] genefilter_1.89.0 later_1.4.1
## [91] splines_4.4.3 dplyr_1.1.4
## [93] lattice_0.22-6 survival_3.8-3
## [95] reader_1.0.6 bit_4.6.0
## [97] annotate_1.85.0 tidyselect_1.2.1
## [99] SingleCellExperiment_1.29.2 locfit_1.5-9.12
## [101] maketools_1.3.2 Biostrings_2.75.4
## [103] scuttle_1.17.0 knitr_1.50
## [105] blockmodeling_1.1.5 IRanges_2.41.3
## [107] edgeR_4.5.9 SummarizedExperiment_1.37.0
## [109] stats4_4.4.3 xfun_0.51
## [111] Biobase_2.67.0 statmod_1.5.0
## [113] brio_1.1.5 matrixStats_1.5.0
## [115] pheatmap_1.0.12 stringi_1.8.4
## [117] UCSC.utils_1.3.1 lazyeval_0.2.2
## [119] yaml_2.3.10 evaluate_1.0.3
## [121] codetools_0.2-20 RcppEigen_0.3.4.0.2
## [123] tibble_3.2.1 BiocManager_1.30.25
## [125] cli_3.6.4 reticulate_1.41.0.1
## [127] shinythemes_1.2.0 xtable_1.8-4
## [129] munsell_0.5.1 jquerylib_0.1.4
## [131] Rcpp_1.0.14 GenomeInfoDb_1.43.4
## [133] tidyverse_2.0.0 png_0.1-8
## [135] XML_3.99-0.18 parallel_4.4.3
## [137] ggplot2_3.5.1 blob_1.2.4
## [139] scran_1.35.0 bitops_1.0-9
## [141] viridisLite_0.4.2 scales_1.3.0
## [143] purrr_1.0.4 crayon_1.5.3
## [145] rlang_1.1.5 KEGGREST_1.47.0
## [147] shinyjs_2.1.0