Continued here due to posting difficulties:

Extract from the results table:

   Inhibitor Vehicle lFC.Av  LogFC ...
F1       0.0    27.1   -Inf  7.768 ...
F2      24.0     0.0    Inf -7.591 ...
...

Swapping Inhibitor and Vehicle in the test.results() call seems to make everything properly consistent, but that contradicts what is says in the documentation for the function:

gp1 The treatment level name.

gp2 The control level name. Should be the factor's reference level. See R function relevel.

sessionInfo( ):

R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Rocky Linux 8.10 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /gpfs3/well/bsg/bjw/conda-envs/mass_spec/lib/libopenblasp-r0.3.30.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=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: Europe/London
tzcode source: system (glibc)

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] vsn_3.74.0            ComplexHeatmap_2.22.0 ggplot2_4.0.1        
 [4] msmsTests_1.44.0      msmsEDA_1.44.0        MSnbase_2.32.0       
 [7] ProtGenerics_1.38.0   S4Vectors_0.44.0      mzR_2.40.0           
[10] Rcpp_1.1.0            Biobase_2.66.0        BiocGenerics_0.52.0  

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          jsonlite_2.0.0             
  [3] shape_1.4.6.1               MultiAssayExperiment_1.32.0
  [5] magrittr_2.0.4              magick_2.9.0               
  [7] farver_2.1.2                MALDIquant_1.22.3          
  [9] GlobalOptions_0.1.3         zlibbioc_1.52.0            
 [11] vctrs_0.6.5                 htmltools_0.5.9            
 [13] S4Arrays_1.6.0              SparseArray_1.6.0          
 [15] mzID_1.44.0                 KernSmooth_2.23-26         
 [17] htmlwidgets_1.6.4           plyr_1.8.9                 
 [19] sandwich_3.1-1              impute_1.80.0              
 [21] zoo_1.8-15                  igraph_2.1.4               
 [23] mime_0.13                   lifecycle_1.0.5            
 [25] iterators_1.0.14            pkgconfig_2.0.3            
 [27] Matrix_1.7-4                R6_2.6.1                   
 [29] fastmap_1.2.0               GenomeInfoDbData_1.2.13    
 [31] MatrixGenerics_1.18.0       shiny_1.12.1               
 [33] clue_0.3-66                 digest_0.6.39              
 [35] pcaMethods_1.98.0           colorspace_2.1-2           
 [37] GenomicRanges_1.58.0        labeling_0.4.3             
 [39] httr_1.4.7                  abind_1.4-8                
 [41] compiler_4.4.3              withr_3.0.2                
 [43] doParallel_1.0.17           S7_0.2.1                   
 [45] BiocParallel_1.40.0         hexbin_1.28.5              
 [47] gplots_3.3.0                MASS_7.3-65                
 [49] DelayedArray_0.32.0         rjson_0.2.23               
 [51] gtools_3.9.5                caTools_1.18.3             
 [53] tools_4.4.3                 PSMatch_1.10.0             
 [55] otel_0.2.0                  httpuv_1.6.16              
 [57] glue_1.8.0                  QFeatures_1.16.0           
 [59] promises_1.5.0              cluster_2.1.8.1            
 [61] reshape2_1.4.5              generics_0.1.4             
 [63] gtable_0.3.6                tzdb_0.5.0                 
 [65] preprocessCore_1.68.0       tidyr_1.3.2                
 [67] hms_1.1.4                   XVector_0.46.0             
 [69] foreach_1.5.2               pillar_1.11.1              
 [71] stringr_1.6.0               limma_3.62.1               
 [73] later_1.4.5                 splines_4.4.3              
 [75] circlize_0.4.17             gmm_1.9-1                  
 [77] dplyr_1.1.4                 lattice_0.22-7             
 [79] tidyselect_1.2.1            locfit_1.5-9.12            
 [81] IRanges_2.40.0              edgeR_4.4.0                
 [83] imputeLCMD_2.1              SummarizedExperiment_1.36.0
 [85] shinydashboard_0.7.3        statmod_1.5.1              
 [87] matrixStats_1.5.0           DT_0.34.0                  
 [89] DEP_1.28.0                  stringi_1.8.7              
 [91] UCSC.utils_1.2.0            lazyeval_0.2.2             
 [93] codetools_0.2-20            qvalue_2.38.0              
 [95] MsCoreUtils_1.18.0          tibble_3.3.0               
 [97] BiocManager_1.30.27         cli_3.6.5                  
 [99] affyio_1.76.0               xtable_1.8-4               
[101] GenomeInfoDb_1.42.0         norm_1.0-11.1              
[103] png_0.1-8                   XML_3.99-0.17              
[105] parallel_4.4.3              readr_2.1.6                
[107] assertthat_0.2.1            AnnotationFilter_1.30.0    
[109] bitops_1.0-9                mvtnorm_1.3-3              
[111] scales_1.4.0                tmvtnorm_1.7               
[113] affy_1.84.0                 ncdf4_1.24                 
[115] purrr_1.2.0                 crayon_1.5.3               
[117] GetoptLong_1.1.0            rlang_1.1.6