Hi, I'm working with R 4.5.0, Bioconductor version 3.21, and DESeq2 1.48.0, and I'm getting the following error:
dds <- DESeqDataSetFromMatrix(
countData = counts,
colData = colData,
design = ~ subjectID + condition # Paired design
)
# converting counts to integer mode
# Error in validObject(.Object) :
# invalid class "DESeqDataSet" object: superclass "ExpData" not defined in the environment of the object's class
I've tried manually reinstalling DESeq2 and its dependencies, Bioconductor, and I even went so far as to do a fresh R install in a new environment, but I'm still getting this bug. Can anybody help? Thanks so much!
Session info:
R version 4.5.0 (2025-04-11) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.6.1
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
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: America/Los_Angeles tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq2_1.48.0 SummarizedExperiment_1.38.1 Biobase_2.68.0
[4] MatrixGenerics_1.20.0 matrixStats_1.5.0 GenomicRanges_1.60.0
[7] GenomeInfoDb_1.44.0 IRanges_2.42.0 S4Vectors_0.46.0
[10] BiocGenerics_0.54.0 generics_0.1.3
loaded via a namespace (and not attached):
[1] Matrix_1.7-3 gtable_0.3.6 jsonlite_2.0.0
[4] dplyr_1.1.4 compiler_4.5.0 crayon_1.5.3
[7] tidyselect_1.2.1 Rcpp_1.0.14 parallel_4.5.0
[10] scales_1.4.0 BiocParallel_1.42.0 lattice_0.22-7
[13] ggplot2_3.5.2 R6_2.6.1 XVector_0.48.0
[16] S4Arrays_1.8.0 tibble_3.2.1 DelayedArray_0.34.1
[19] GenomeInfoDbData_1.2.14 pillar_1.10.2 RColorBrewer_1.1-3
[22] rlang_1.1.6 SparseArray_1.8.0 cli_3.6.5
[25] magrittr_2.0.3 locfit_1.5-9.12 grid_4.5.0
[28] lifecycle_1.0.4 vctrs_0.6.5 glue_1.8.0
[31] farver_2.1.2 codetools_0.2-20 abind_1.4-8
[34] httr_1.4.7 pkgconfig_2.0.3 tools_4.5.0
[37] UCSC.utils_1.4.0
I just ran into the same issue. I also tried fresh install and I reran code from the DESeq2 vignette (Transcript abundance files and tximport / tximeta) and it got the same error.
R version 4.5.0 (2025-04-11) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.4.1
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
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: America/New_York tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] readr_2.1.5 limma_3.64.0
[3] goseq_1.60.0 geneLenDataBase_1.44.0
[5] BiasedUrn_2.0.12 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[7] org.Mm.eg.db_3.21.0 tximport_1.36.0
[9] GenomicAlignments_1.44.0 Rsamtools_2.24.0
[11] Biostrings_2.76.0 XVector_0.48.0
[13] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 GenomicFeatures_1.60.0
[15] AnnotationDbi_1.70.0 DESeq2_1.48.0
[17] SummarizedExperiment_1.38.1 Biobase_2.68.0
[19] MatrixGenerics_1.20.0 matrixStats_1.5.0
[21] GenomicRanges_1.60.0 GenomeInfoDb_1.44.0
[23] IRanges_2.42.0 S4Vectors_0.46.0
[25] BiocGenerics_0.54.0 generics_0.1.3
loaded via a namespace (and not attached): [1] DBI_1.2.3 bitops_1.0-9 httr2_1.1.2
[4] biomaRt_2.64.0 rlang_1.1.6 magrittr_2.0.3
[7] compiler_4.5.0 RSQLite_2.3.11 mgcv_1.9-3
[10] png_0.1-8 vctrs_0.6.5 txdbmaker_1.4.1
[13] stringr_1.5.1 pkgconfig_2.0.3 crayon_1.5.3
[16] fastmap_1.2.0 dbplyr_2.5.0 rmarkdown_2.29
[19] tzdb_0.5.0 UCSC.utils_1.4.0 bit_4.6.0
[22] xfun_0.52 cachem_1.1.0 jsonlite_2.0.0
[25] progress_1.2.3 blob_1.2.4 DelayedArray_0.34.1
[28] BiocParallel_1.42.0 parallel_4.5.0 prettyunits_1.2.0
[31] R6_2.6.1 stringi_1.8.7 RColorBrewer_1.1-3
[34] rtracklayer_1.68.0 Rcpp_1.0.14 knitr_1.50
[37] Matrix_1.7-3 splines_4.5.0 tidyselect_1.2.1
[40] abind_1.4-8 yaml_2.3.10 codetools_0.2-20
[43] curl_6.2.2 lattice_0.22-7 tibble_3.2.1
[46] withr_3.0.2 KEGGREST_1.48.0 evaluate_1.0.3
[49] BiocFileCache_2.16.0 xml2_1.3.8 pillar_1.10.2
[52] BiocManager_1.30.25 filelock_1.0.3 vroom_1.6.5
[55] RCurl_1.98-1.17 hms_1.1.3 ggplot2_3.5.2
[58] scales_1.4.0 glue_1.8.0 tools_4.5.0
[61] BiocIO_1.18.0 locfit_1.5-9.12 XML_3.99-0.18
[64] grid_4.5.0 colorspace_2.1-1 nlme_3.1-168
[67] GenomeInfoDbData_1.2.14 restfulr_0.0.15 cli_3.6.5
[70] rappdirs_0.3.3 S4Arrays_1.8.0 dplyr_1.1.4
[73] gtable_0.3.6 digest_0.6.37 SparseArray_1.8.0
[76] rjson_0.2.23 farver_2.1.2 memoise_2.0.1
[79] htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7
[82] statmod_1.5.0 GO.db_3.21.0 bit64_4.6.0-1
Posted also here
https://github.com/thelovelab/DESeq2/issues/112
I have bumped the version number in release which should resolve the issue once it propagates.