Hi everyone,

I was performing some DEGs and got this message:

Warning messages:
1: In nbinomGLM(x = x, Y = YNZ, size = size, weights = weightsNZ,  ... :
  the line search routine failed, possibly due to insufficient numeric precision

I've realized it was something related with the negative binomial model. But how can I solve this?

Thanks.

sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default


locale:
[1] LC_COLLATE=Portuguese_Portugal.1252  LC_CTYPE=Portuguese_Portugal.1252   
[3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C                        
[5] LC_TIME=Portuguese_Portugal.1252    

time zone: Europe/Lisbon
tzcode source: internal

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

other attached packages:
 [1] crayon_1.5.2                biomaRt_2.56.1              reshape2_1.4.4             
 [4] lubridate_1.9.2             forcats_1.0.0               stringr_1.5.0              
 [7] dplyr_1.1.2                 purrr_1.0.1                 readr_2.1.4                
[10] tidyr_1.3.0                 tibble_3.2.1                tidyverse_2.0.0            
[13] ggplot2_3.4.2               DESeq2_1.40.1               SummarizedExperiment_1.30.2
[16] Biobase_2.60.0              MatrixGenerics_1.12.2       matrixStats_1.0.0          
[19] GenomicRanges_1.52.0        GenomeInfoDb_1.36.0         IRanges_2.34.0             
[22] S4Vectors_0.38.1            BiocGenerics_0.46.0        

loaded via a namespace (and not attached):
  [1] rstudioapi_0.14         xlsx_0.6.5              magrittr_2.0.3         
  [4] farver_2.1.1            rmarkdown_2.22          fs_1.6.2               
  [7] zlibbioc_1.46.0         vctrs_0.6.3             memoise_2.0.1          
 [10] RCurl_1.98-1.12         usethis_2.2.0           htmltools_0.5.5        
 [13] S4Arrays_1.0.4          progress_1.2.2          curl_5.0.1             
 [16] cellranger_1.1.0        desc_1.4.2              htmlwidgets_1.6.2      
 [19] plyr_1.8.8              cachem_1.0.8            mime_0.12              
 [22] lifecycle_1.0.3         pkgconfig_2.0.3         Matrix_1.5-4.1         
 [25] R6_2.5.1                fastmap_1.1.1           GenomeInfoDbData_1.2.10
 [28] shiny_1.7.4             digest_0.6.31           numDeriv_2016.8-1.1    
 [31] colorspace_2.1-0        AnnotationDbi_1.62.1    ps_1.7.5               
 [34] rprojroot_2.0.3         pkgload_1.3.2           RSQLite_2.3.1          
 [37] filelock_1.0.2          labeling_0.4.2          fansi_1.0.4            
 [40] timechange_0.2.0        httr_1.4.6              compiler_4.3.0         
 [43] remotes_2.4.2           bit64_4.0.5             withr_2.5.0            
 [46] BiocParallel_1.34.2     DBI_1.1.3               pkgbuild_1.4.1         
 [49] MASS_7.3-60             rappdirs_0.3.3          DelayedArray_0.26.3    
 [52] sessioninfo_1.2.2       tools_4.3.0             httpuv_1.6.11          
 [55] glue_1.6.2              callr_3.7.3             promises_1.2.0.1       
 [58] grid_4.3.0              generics_0.1.3          gtable_0.3.3           
 [61] tzdb_0.4.0              hms_1.1.3               xml2_1.3.4             
 [64] utf8_1.2.3              XVector_0.40.0          pillar_1.9.0           
 [67] emdbook_1.3.12          later_1.3.1             rJava_1.0-6            
 [70] BiocFileCache_2.8.0     lattice_0.21-8          bit_4.0.5              
 [73] tidyselect_1.2.0        locfit_1.5-9.8          Biostrings_2.68.1      
 [76] miniUI_0.1.1.1          knitr_1.43              xfun_0.39              
 [79] devtools_2.4.5          stringi_1.7.12          yaml_2.3.7             
 [82] evaluate_0.21           codetools_0.2-19        xlsxjars_0.6.1         
 [85] bbmle_1.0.25            cli_3.6.1               xtable_1.8-4           
 [88] munsell_0.5.0           processx_3.8.1          Rcpp_1.0.10            
 [91] readxl_1.4.2            dbplyr_2.3.2            coda_0.19-4            
 [94] png_0.1-8               bdsmatrix_1.3-6         XML_3.99-0.14          
 [97] parallel_4.3.0          ellipsis_0.3.2          blob_1.2.4             
[100] prettyunits_1.1.1       profvis_0.3.8           urlchecker_1.0.1       
[103] bitops_1.0-7            mvtnorm_1.2-2           apeglm_1.22.1          
[106] scales_1.2.1            rlang_1.1.1             KEGGREST_1.40.0

Try removing low count genes.