gksmyth
commented
8 months ago Ah, thanks for alerting me. Absolutely it was not my intention to change any edgeR defaults in the release version of edgeR. Six days ago I was fixing a bug in the legacy=FALSE glmQLFit.default pipeline and I accidentally overwrote the release version of glmQLFit with the devel version while doing that. Or rather, I forgot that I needed to keep them distinct. My apologies.
I have now repaired my mistake and reset the default back to legacy=TRUE in edgeR 4.0.10. You should be able to get it from git already, otherwise it should be reflected in BiocManager::install in a few days.
PeteHaitch
alanocallaghan
From edgeR news file:
Recently, the default changed from
legacy=TRUEtolegacy=FALSEin the release branch (BioC 3.18): https://code.bioconductor.org/browse/edgeR/commit/1f0de5e1fa24e436315e13fad517e1bdac502fdd @gksmyth: It's a bit unexpected for the default value to change in the release version, so I'd like to confirm that this change was intended for the release version (BioC 3.18) and not just the devel version (BioC 3.19) of edgeR?@LTLA, @alanocallaghan: With regards to
inst/book/cluster-abundance.Rmdin OSCA.multisample, we can revert to the previous behaviour just by addinglegacy=TRUEin the appropriate places which seems the best solution for BioC 3.18 (I'll make a PR). For BioC 3.19, we can either adapt the text to the new results (i.e. use the defaultlegacy=FALSE) or stick with the old results and text (i.e. also makelegacy=TRUE).Example based on
inst/book/cluster-abundance.RmdExtract example and setup DGEList object
Performing the DA analysis
Assuming most labels do not change
Removing the offending labels
Testing against a log-fold change threshold
Session info
``` r sessionInfo() #> R version 4.3.2 (2023-10-31) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: CentOS Linux 7 (Core) #> #> Matrix products: default #> BLAS: /stornext/System/data/apps/R/R-4.3.2/lib64/R/lib/libRblas.so #> LAPACK: /stornext/System/data/apps/R/R-4.3.2/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C #> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 #> [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: Australia/Melbourne #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats4 stats graphics grDevices utils datasets methods #> [8] base #> #> other attached packages: #> [1] edgeR_4.0.9 limma_3.58.1 #> [3] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 #> [5] Biobase_2.62.0 GenomicRanges_1.54.1 #> [7] GenomeInfoDb_1.38.5 IRanges_2.36.0 #> [9] S4Vectors_0.40.2 BiocGenerics_0.48.1 #> [11] MatrixGenerics_1.14.0 matrixStats_1.2.0 #> [13] rebook_1.12.0 #> #> loaded via a namespace (and not attached): #> [1] SparseArray_1.2.3 bitops_1.0-7 lattice_0.22-5 #> [4] digest_0.6.34 evaluate_0.23 grid_4.3.2 #> [7] fastmap_1.1.1 Matrix_1.6-5 graph_1.80.0 #> [10] BiocManager_1.30.22 XML_3.99-0.16 codetools_0.2-19 #> [13] abind_1.4-5 cli_3.6.2 CodeDepends_0.6.5 #> [16] rlang_1.1.3 crayon_1.5.2 BiocStyle_2.30.0 #> [19] XVector_0.42.0 splines_4.3.2 reprex_2.1.0 #> [22] withr_3.0.0 DelayedArray_0.28.0 yaml_2.3.8 #> [25] S4Arrays_1.2.0 tools_4.3.2 dir.expiry_1.10.0 #> [28] locfit_1.5-9.8 GenomeInfoDbData_1.2.11 filelock_1.0.3 #> [31] lifecycle_1.0.4 zlibbioc_1.48.0 fs_1.6.3 #> [34] glue_1.7.0 Rcpp_1.0.12 statmod_1.5.0 #> [37] xfun_0.41 rstudioapi_0.15.0 knitr_1.45 #> [40] htmltools_0.5.7 rmarkdown_2.25 compiler_4.3.2 #> [43] RCurl_1.98-1.14 ```