Error when running DESeqDataSetFromMatrix inside Rstudio or inside a loop #117
Description
Hi,
Since a week ago, I have beeing facing this error when rerunning old Rmd files that used to work without any issue:
dds <- DESeqDataSetFromMatrix(countData=as.matrix(round(countData)), colData=metaData, design= ~ dex )
Returns this error when executed inside Rstudio in a Rmarkdown or when trying to Knit it into an html:
converting counts to integer mode Error in validObject(.Object) : invalid class “DESeqDataSet” object: 'NAMES' slot must be set to NULL at all time
BUT, when running it in the terminal using same R version and same DESEQ2 version, it runs without errors. The error returns inside the terminal when running the function inside a loop, like in this example which used to work before:
metaData$dex <- as.factor(metaData$dex)
for(i in 1:(length(levels(metaData$dex)))){
dex1 <- levels(metaData$dex)[i]
metaData$tmp <- as.character(metaData$dex)
metaData$tmp[metaData$tmp != dex1] <- "others"
metaData$tmp <- as.factor(metaData$tmp)
dds <- DESeqDataSetFromMatrix(countData=round(countData),
colData=metaData,
design= ~ tmp )
}
Why is this happening?
This is my session.info():
> sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Madrid
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggrepel_0.9.6 dplyr_1.1.4
[3] ggplot2_3.5.2 DESeq2_1.48.1
[5] SummarizedExperiment_1.38.1 Biobase_2.68.0
[7] MatrixGenerics_1.20.0 matrixStats_1.5.0
[9] GenomicRanges_1.60.0 GenomeInfoDb_1.44.1
[11] IRanges_2.42.0 S4Vectors_0.46.0
[13] 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] compiler_4.5.1 crayon_1.5.3 tidyselect_1.2.1
[7] Rcpp_1.1.0 parallel_4.5.1 scales_1.3.0
[10] BiocParallel_1.42.1 lattice_0.22-7 R6_2.6.1
[13] XVector_0.48.0 S4Arrays_1.8.1 tibble_3.2.1
[16] DelayedArray_0.34.1 munsell_0.5.1 GenomeInfoDbData_1.2.14
[19] pillar_1.11.0 rlang_1.1.6 SparseArray_1.8.1
[22] cli_3.6.5 withr_3.0.2 magrittr_2.0.3
[25] locfit_1.5-9.12 grid_4.5.1 lifecycle_1.0.4
[28] vctrs_0.6.5 glue_1.8.0 codetools_0.2-20
[31] abind_1.4-8 colorspace_2.1-1 httr_1.4.7
[34] pkgconfig_2.0.3 tools_4.5.1 UCSC.utils_1.4.0