limma_result_categories
Thomas Rauter
2025-01-21
Source:vignettes/limma_result_categories.Rmd
limma_result_categories.Rmd
limma Result Categories
limma analysis results can be divided into three categories, which are defined in this document:
Time Effect: This category focuses on the changes of the feature (e.g. protein) value that occur over time within a single condition.
Average Difference Between Conditions: This category compares the average feature values for levels within a condition, regardless of time.
Interaction Between Condition and Time: This category examines the interaction between time and condition. It identifies features whose value changes differently over time depending on the condition.
Legend:
- A hit is a feature (e.g. a protein) that is significantly changed over time.
- Levels are the different factors of a condition of the experiment. For example, bioreactor phase is a condition, and exponential and stationary are levels within that condition.
Category 1 (time effect)
Temporal pattern within level for a given feature → Hit
Category 2 (average difference conditions)
Overall mean difference between levels for a given feature → Hit
Category 3 (interaction condition & time)
Treatment interacting with time for a feature (time effect changing with treatment, the feature must have different temporal patterns in both conditions/levels) → Hit
Session Info
## R version 4.3.3 (2024-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.5 LTS
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## Matrix products: default
## BLAS: /usr/local/R-4.3.3/lib/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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## time zone: Europe/Vienna
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats graphics grDevices datasets utils methods base
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## loaded via a namespace (and not attached):
## [1] digest_0.6.37 desc_1.4.3 R6_2.6.1
## [4] fastmap_1.2.0 xfun_0.50 cachem_1.1.0
## [7] knitr_1.49 htmltools_0.5.8.1 rmarkdown_2.29
## [10] lifecycle_1.0.4 cli_3.6.4 sass_0.4.9
## [13] pkgdown_2.1.1 textshaping_1.0.0 jquerylib_0.1.4
## [16] renv_1.1.1 systemfonts_1.2.1 compiler_4.3.3
## [19] rstudioapi_0.17.1 tools_4.3.3 ragg_1.3.3
## [22] bslib_0.9.0 evaluate_1.0.3 yaml_2.3.10
## [25] BiocManager_1.30.25 jsonlite_1.8.9 htmlwidgets_1.6.4
## [28] rlang_1.1.5 fs_1.6.5