Unclear DEseq2 replaceOutliers error message
1
0
Entering edit mode
Pak • 0
@707d2c58
Last seen 4 months ago
United States

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
DESeq2 • 389 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 day ago
United States

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1056 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6