Example analyses of a small human RNA-seq dataset to exemplify common challenges in the data that need to be taken into account.
Data and metadata available as R objects in the filesdata.rds and metadata.rds.
sessionInfo() output:
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Fedora Linux 35 (Workstation Edition)
Matrix products: default
BLAS/LAPACK: /data-old/user/adesous1/my-envs/r403/lib/libopenblasp-r0.3.18.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.3.5 Matrix_1.4-1
loaded via a namespace (and not attached):
[1] lattice_0.20-45 fansi_1.0.3 withr_2.5.0 utf8_1.2.2 crayon_1.5.1 grid_4.0.3 R6_2.5.1
[8] lifecycle_1.0.1 gtable_0.3.0 magrittr_2.0.3 scales_1.1.1 pillar_1.7.0 rlang_1.0.2 cli_3.2.0
[15] vctrs_0.4.0 ellipsis_0.3.2 tools_4.0.3 glue_1.6.2 munsell_0.5.0 xfun_0.30 compiler_4.0.3
[22] pkgconfig_2.0.3 colorspace_2.0-3 knitr_1.38 tibble_3.1.6
References: [1] Lonsdale, J., Thomas, J., Salvatore, M. et al. The Genotype-Tissue Expression (GTEx) project. Nat Genet 45, 580�585 (2013). https://doi.org/10.1038/ng.2653