I have a comparison of 6 groups: healthy, disease, longer_disease, treatment1, treatment2, treatment3. I have previously used LRT. I can consider longer_disease as the group to compare to, and I am only interested in comparing the rest of groups to that one, not in every individual comparison.

I have used LRT before in other dataset and I did not have this observation. On re-running (and re-reading) about it, I get the same number of DEGs in each individual comparison (e.g. treatment1_vs_longer_disease or treatment2_vs_longer_disease).

Should I use Wald... how?

Thank you! Help!

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design = ~ group)

#where group is the factor of 5 variables 
dds$group <- relevel(dds$group, ref = "longer_disease") # to set it as my baseline (this makes sense biololgically and for our question)

keep <- rowSums(counts(dds) >= 10) >= 5 # since I have a minimum of 5 biological replicates per group
dds <- dds[keep,]

dds <- DESeq(dds, test="LRT", reduced=~1) # considering our design is comparing between groups 
res <- results(dds)

resultsNames(dds)
[1] "Intercept"             "group_treatment1_vs_longer_disease"    
[3] "group_healthy_vs_longer_disease" "group_treatment2_vs_longer_disease"    
[5] "group_treatment2_vs_longer_disease"  "group_disease_vs_longer_disease"

# please also include the results of running the following in an R session 

sessionInfo( )

R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Monterey 12.6.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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

time zone: Europe/London
tzcode source: internal

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

other attached packages:
 [1] lubridate_1.9.4            
 [2] forcats_1.0.0              
 [3] stringr_1.5.1              
 [4] dplyr_1.1.4                
 [5] purrr_1.0.4                
 [6] readr_2.1.5                
 [7] tidyr_1.3.1                
 [8] tibble_3.2.1               
 [9] ggplot2_3.5.2              
[10] tidyverse_2.0.0            
[11] VennDiagram_1.7.3          
[12] futile.logger_1.4.3        
[13] pheatmap_1.0.12            
[14] DESeq2_1.44.0              
[15] SummarizedExperiment_1.34.0
[16] Biobase_2.64.0             
[17] MatrixGenerics_1.16.0      
[18] matrixStats_1.5.0          
[19] GenomicRanges_1.56.2       
[20] GenomeInfoDb_1.40.1        
[21] IRanges_2.38.1             
[22] S4Vectors_0.42.1           
[23] BiocGenerics_0.50.0        

loaded via a namespace (and not attached):
 [1] gtable_0.3.6            lattice_0.22-7         
 [3] tzdb_0.5.0              vctrs_0.6.5            
 [5] tools_4.4.1             generics_0.1.4         
 [7] parallel_4.4.1          pkgconfig_2.0.3        
 [9] Matrix_1.7-3            RColorBrewer_1.1-3     
[11] lifecycle_1.0.4         GenomeInfoDbData_1.2.12
[13] compiler_4.4.1          farver_2.1.2           
[15] codetools_0.2-20        pillar_1.10.2          
[17] crayon_1.5.3            BiocParallel_1.38.0    
[19] DelayedArray_0.30.1     abind_1.4-8            
[21] tidyselect_1.2.1        locfit_1.5-9.12        
[23] stringi_1.8.7           labeling_0.4.3         
[25] colorspace_2.1-1        cli_3.6.5              
[27] SparseArray_1.4.8       magrittr_2.0.3         
[29] S4Arrays_1.4.1          utf8_1.2.5             
[31] withr_3.0.2             scales_1.4.0           
[33] UCSC.utils_1.0.0        bit64_4.6.0-1          
[35] timechange_0.3.0        lambda.r_1.2.4         
[37] XVector_0.44.0          httr_1.4.7             
[39] bit_4.6.0               hms_1.1.3              
[41] rlang_1.1.6             futile.options_1.0.1   
[43] Rcpp_1.0.14             glue_1.8.0             
[45] BiocManager_1.30.25     formatR_1.14           
[47] vroom_1.6.5             rstudioapi_0.17.1      
[49] jsonlite_2.0.0          R6_2.6.1               
[51] zlibbioc_1.50.0