Hello,

I have a question regarding the results output of the Wald test I'm running in DESeq2. I have time-series data with samples collected at 5 time points b/w 2 genotypes: 0hr, 2hr, 6hr, 12hr, 24hr and mutant vs. control. My question is this: using the design in my code below, how is the Log2FoldChange calculated in the results table, considering that there are multiple time points with every gene? Is it the average log2 fold change across all time points per gene?

dds <- DESeqDataSetFromMatrix(countData = ctdata, colData = cldata, design = ~ genotype + time)
dds <- dds[rowSums(counts(dds) > 10,]
dds_res <- results(dds)

sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] DEGreport_1.28.0            gplots_3.1.1                VennDiagram_1.6.20          futile.logger_1.4.3         WGCNA_1.70-3               
 [6] fastcluster_1.2.3           dynamicTreeCut_1.63-1       WebGestaltR_0.4.4           pheatmap_1.0.12             ggpubr_0.4.0               
[11] openxlsx_4.2.4              BiocParallel_1.26.2         ggrepel_0.9.1               forcats_0.5.1               stringr_1.4.0              
[16] dplyr_1.0.7                 purrr_0.3.4                 readr_2.0.1                 tidyr_1.1.3                 tibble_3.1.4               
[21] ggplot2_3.3.5               tidyverse_1.3.1             DESeq2_1.32.0               SummarizedExperiment_1.22.0 Biobase_2.52.0             
[26] MatrixGenerics_1.4.3        matrixStats_0.60.1          GenomicRanges_1.44.0        GenomeInfoDb_1.28.2         IRanges_2.26.0             
[31] S4Vectors_0.30.0            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  tidyselect_1.1.1            RSQLite_2.2.8               AnnotationDbi_1.54.1        htmlwidgets_1.5.3          
  [6] munsell_0.5.0               codetools_0.2-18            preprocessCore_1.54.0       withr_2.4.2                 colorspace_2.0-2           
 [11] knitr_1.33                  rstudioapi_0.13             ggsignif_0.6.2              labeling_0.4.2              lasso2_1.2-21.1            
 [16] GenomeInfoDbData_1.2.6      mnormt_2.0.2                farver_2.1.0                bit64_4.0.5                 vctrs_0.3.8                
 [21] generics_0.1.0              lambda.r_1.2.4              xfun_0.25                   R6_2.5.1                    doParallel_1.0.16          
 [26] clue_0.3-59                 locfit_1.5-9.4              reshape_0.8.8               bitops_1.0-7                cachem_1.0.6               
 [31] DelayedArray_0.18.0         assertthat_0.2.1            vroom_1.5.4                 scales_1.1.1                nnet_7.3-16                
 [36] gtable_0.3.0                Cairo_1.5-12.2              rlang_0.4.11                genefilter_1.74.0           systemfonts_1.0.2          
 [41] GlobalOptions_0.1.2         rstatix_0.7.0               impute_1.66.0               broom_0.7.9                 checkmate_2.0.0            
 [46] abind_1.4-5                 modelr_0.1.8                backports_1.2.1             Hmisc_4.5-0                 tools_4.1.0                
 [51] psych_2.1.6                 logging_0.10-108            ellipsis_0.3.2              RColorBrewer_1.1-2          ggdendro_0.1.22            
 [56] plyr_1.8.6                  Rcpp_1.0.7                  base64enc_0.1-3             zlibbioc_1.38.0             RCurl_1.98-1.4             
 [61] rpart_4.1-15                GetoptLong_1.0.5            cowplot_1.1.1               haven_2.4.3                 cluster_2.1.2              
 [66] fs_1.5.0                    apcluster_1.4.8             magrittr_2.0.1              data.table_1.14.0           futile.options_1.0.1       
 [71] circlize_0.4.13             reprex_2.0.1                tmvnsim_1.0-2               whisker_0.4                 hms_1.1.0                  
 [76] xtable_1.8-4                XML_3.99-0.7                rio_0.5.27                  jpeg_0.1-9                  readxl_1.3.1               
 [81] gridExtra_2.3               shape_1.4.6                 compiler_4.1.0              KernSmooth_2.23-20          crayon_1.4.1               
 [86] htmltools_0.5.2             mgcv_1.8-36                 tzdb_0.1.2                  Formula_1.2-4               geneplotter_1.70.0         
 [91] lubridate_1.7.10            DBI_1.1.1                   formatR_1.11                dbplyr_2.1.1                ComplexHeatmap_2.8.0       
 [96] MASS_7.3-54                 Matrix_1.3-4                car_3.0-11                  cli_3.0.1                   igraph_1.2.6               
[101] pkgconfig_2.0.3             foreign_0.8-81              xml2_1.3.2                  foreach_1.5.1               svglite_2.0.0              
[106] annotate_1.70.0             rngtools_1.5                XVector_0.32.0              rvest_1.0.1                 doRNG_1.8.2                
[111] digest_0.6.27               ConsensusClusterPlus_1.56.0 Biostrings_2.60.2           cellranger_1.1.0            htmlTable_2.2.1            
[116] edgeR_3.34.0                curl_4.3.2                  gtools_3.9.2                rjson_0.2.20                nlme_3.1-152               
[121] lifecycle_1.0.0             jsonlite_1.7.2              carData_3.0-4               limma_3.48.3                fansi_0.5.0                
[126] pillar_1.6.2                lattice_0.20-44             Nozzle.R1_1.1-1             KEGGREST_1.32.0             fastmap_1.1.0              
[131] httr_1.4.2                  survival_3.2-13             GO.db_3.13.0                glue_1.4.2                  zip_2.2.0                  
[136] png_0.1-7                   iterators_1.0.13            bit_4.0.4                   stringi_1.7.4               blob_1.2.2                 
[141] latticeExtra_0.6-29         caTools_1.18.2              memoise_2.0.0

In plain, not statistically technical language:

When you run DESeq2 with a series of numerical colData like time or dosage, what's returned is not a Log2fold change, but the slope of the line of the normalized, logged data.