I'm running DESeq2 on an RNA-seq dataset with 25 samples divided into 2 clusters (9 and 16). The DESeq2 object was created without any issues, but when I run DEseq, I get the following error from replaceOutliers: Any help is appreciated.

design(dds_select_time ) <- ~ cluster + batch
dds_select_time <- DESeq(dds_select_time )

Error message

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

Error in mcols(colData(object), use.names = TRUE)["replaceable", ] <- DataFrame(type = "intermediate",  : 
  invalid type/length (S4/0) in vector allocation
3.
replaceOutliers(object, minReplicates = minReplicatesForReplace) at core.R#2513
2.
refitWithoutOutliers(object, test = test, betaPrior = betaPrior,
full = full, reduced = reduced, quiet = quiet, minReplicatesForReplace = minReplicatesForReplace,
modelMatrix = modelMatrix, modelMatrixType = modelMatrixType) at core.R#428
1.
DESeq(dds_select_time)

sessionInfo( )
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

other attached packages:
 [1] plotly_4.10.4               writexl_1.5.4               ggalluvial_0.12.5           cowplot_1.1.3               corrplot_0.95               dtwclust_6.0.0             
 [7] dtw_1.23-1                  proxy_0.4-27                DESeq2_1.46.0               SummarizedExperiment_1.36.0 Biobase_2.66.0              MatrixGenerics_1.18.1      
[13] matrixStats_1.5.0           GenomicRanges_1.58.0        GenomeInfoDb_1.42.3         IRanges_2.40.1              S4Vectors_0.44.0            BiocGenerics_0.52.0        
[19] pheatmap_1.0.12             lubridate_1.9.3             forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.4                
[25] readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1                ggplot2_3.5.1               tidyverse_2.0.0             readxl_1.4.3               

loaded via a namespace (and not attached):
 [1] rlang_1.1.5             magrittr_2.0.3          clue_0.3-66             flexclust_1.5.0         compiler_4.4.2          vctrs_0.6.5             reshape2_1.4.4         
 [8] pkgconfig_2.0.3         crayon_1.5.3            fastmap_1.2.0           XVector_0.46.0          labeling_0.4.3          utf8_1.2.4              promises_1.3.2         
[15] rmarkdown_2.29          tzdb_0.4.0              UCSC.utils_1.2.0        xfun_0.52               modeltools_0.2-24       zlibbioc_1.52.0         jsonlite_1.8.9         
[22] later_1.4.1             DelayedArray_0.32.0     BiocParallel_1.40.2     parallel_4.4.2          cluster_2.1.8           R6_2.5.1                stringi_1.8.4          
[29] RColorBrewer_1.1-3      cellranger_1.1.0        Rcpp_1.0.14             iterators_1.0.14        knitr_1.50              httpuv_1.6.15           Matrix_1.7-1           
[36] timechange_0.3.0        tidyselect_1.2.1        rstudioapi_0.16.0       abind_1.4-8             yaml_2.3.10             codetools_0.2-19        lattice_0.22-5         
[43] plyr_1.8.9              shiny_1.10.0            withr_3.0.2             evaluate_1.0.3          RcppParallel_5.1.10     pillar_1.10.1           renv_1.1.4             
[50] foreach_1.5.2           shinyjs_2.1.0           generics_0.1.3          rprojroot_2.0.4         hms_1.1.3               munsell_0.5.1           scales_1.3.0           
[57] xtable_1.8-4            class_7.3-23            glue_1.8.0              lazyeval_0.2.2          tools_4.4.2             data.table_1.16.4       RSpectra_0.16-2        
[64] locfit_1.5-9.12         grid_4.4.2              crosstalk_1.2.1         colorspace_2.1-1        GenomeInfoDbData_1.2.13 cli_3.6.3               viridisLite_0.4.2      
[71] S4Arrays_1.6.0          gtable_0.3.6            digest_0.6.37           SparseArray_1.6.2       ggrepel_0.9.6           htmlwidgets_1.6.4       farver_2.1.2           
[78] htmltools_0.5.8.1       lifecycle_1.0.4         httr_1.4.7              here_1.0.1              mime_0.12

I'm not sure exactly about that error, it may be due to the object being created in a different way. Again not sure.

But you can avoid the error with minRep = Inf which will avoid replacement. I'm not a big fan of automatic outlier replacement, although we included it. I usually turn it off.