Hi, I have run DESeq2 in the past without any problem until recently. I have installed the newest version of R and DESeq2 in my new computer and I started getting the error below:
dds <- DESeqDataSetFromMatrix(countData = cnts,
+ colData = coldata,
+ design = ~ Phenotype)
Error in SummarizedExperiment(assays = SimpleList(counts = countData), :
the rownames and colnames of the supplied assay(s) must be NULL or
identical to those of the SummarizedExperiment object (or derivative)
to construct
It will be great to get some help/hints on what's going on with my freshly installed DESeq2.
I run the DESeq2 in my old machine and it runs without issues which means that the column names in the counts are same as the row names of the coldata (sample information).
> SummarizedExperiment::SummarizedExperiment()
class: SummarizedExperiment
dim: 0 0
metadata(0):
assays(0):
rownames: NULL
rowData names(0):
colnames: NULL
colData names(0):
> getClass("SummarizedExperiment")
Class "SummarizedExperiment" [package "SummarizedExperiment"]
Slots:
Name: colData assays NAMES elementMetadata
Class: DataFrame Assays_OR_NULL character_OR_NULL DataFrame
Name: metadata
Class: list
Extends:
Class "RectangularData", directly
Class "Vector", directly
Class "Annotated", by class "Vector", distance 2
Class "vector_OR_Vector", by class "Vector", distance 2
Known Subclasses:
Class "RangedSummarizedExperiment", directly, with explicit coerce
Checking with BiocManager::valid()
> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
[1] TRUE
Is there anything obvious I am missing here? Many thanks in advance!
Here you can have a look at the version of the packages I am using
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] DESeq2_1.38.2 SummarizedExperiment_1.28.0
[3] MatrixGenerics_1.10.0 matrixStats_0.63.0
[5] GenomicRanges_1.50.2 GenomeInfoDb_1.34.4
[7] plyr_1.8.8 pander_0.6.5
[9] data.table_1.14.6 tradeSeq_1.12.0
[11] forcats_0.5.2 stringr_1.5.0
[13] dplyr_1.0.10 purrr_1.0.0
[15] readr_2.1.3 tidyr_1.2.1
[17] tibble_3.1.8 tidyverse_1.3.2
[19] gprofiler2_0.2.1 ComplexHeatmap_2.14.0
[21] Glimma_2.8.0 RColorBrewer_1.1-3
[23] EnhancedVolcano_1.16.0 ggrepel_0.9.2
[25] ggplot2_3.4.0 org.Hs.eg.db_3.16.0
[27] AnnotationDbi_1.60.0 IRanges_2.32.0
[29] S4Vectors_0.36.1 Biobase_2.58.0
[31] BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] googledrive_2.0.0 colorspace_2.0-3
[3] rjson_0.2.21 ellipsis_0.3.2
[5] circlize_0.4.15 XVector_0.38.0
[7] GlobalOptions_0.1.2 fs_1.5.2
[9] clue_0.3-63 rstudioapi_0.14
[11] bit64_4.0.5 fansi_1.0.3
[13] lubridate_1.9.0 xml2_1.3.3
[15] splines_4.2.2 codetools_0.2-18
[17] doParallel_1.0.17 cachem_1.0.6
[19] geneplotter_1.76.0 jsonlite_1.8.4
[21] broom_1.0.2 annotate_1.76.0
[23] cluster_2.1.4 dbplyr_2.2.1
[25] png_0.1-8 BiocManager_1.30.19
[27] compiler_4.2.2 httr_1.4.4
[29] backports_1.4.1 assertthat_0.2.1
[31] Matrix_1.5-3 fastmap_1.1.0
[33] lazyeval_0.2.2 gargle_1.2.1
[35] limma_3.54.0 cli_3.5.0
[37] htmltools_0.5.4 tools_4.2.2
[39] igraph_1.3.5 gtable_0.3.1
[41] glue_1.6.2 GenomeInfoDbData_1.2.9
[43] Rcpp_1.0.9 cellranger_1.1.0
[45] vctrs_0.5.1 Biostrings_2.66.0
[47] nlme_3.1-161 iterators_1.0.14
[49] slingshot_2.6.0 rvest_1.0.3
[51] timechange_0.1.1 lifecycle_1.0.3
[53] TrajectoryUtils_1.6.0 XML_3.99-0.13
[55] googlesheets4_1.0.1 princurve_2.1.6
[57] edgeR_3.40.1 zlibbioc_1.44.0
[59] scales_1.2.1 hms_1.1.2
[61] parallel_4.2.2 SingleCellExperiment_1.20.0
[63] pbapply_1.6-0 gridExtra_2.3
[65] memoise_2.0.1 stringi_1.7.8
[67] RSQLite_2.2.19 foreach_1.5.2
[69] BiocParallel_1.32.4 shape_1.4.6
[71] rlang_1.0.6 pkgconfig_2.0.3
[73] bitops_1.0-7 lattice_0.20-45
[75] htmlwidgets_1.6.0 bit_4.0.5
[77] tidyselect_1.2.0 magrittr_2.0.3
[79] R6_2.5.1 generics_0.1.3
[81] DelayedArray_0.24.0 DBI_1.1.3
[83] mgcv_1.8-41 pillar_1.8.1
[85] haven_2.5.1 withr_2.5.0
[87] KEGGREST_1.38.0 RCurl_1.98-1.9
[89] modelr_0.1.10 crayon_1.5.2
[91] utf8_1.2.2 plotly_4.10.1
[93] tzdb_0.3.0 viridis_0.6.2
[95] GetoptLong_1.0.5 locfit_1.5-9.6
[97] readxl_1.4.1 blob_1.2.3
[99] reprex_2.0.2 digest_0.6.31
[101] xtable_1.8-4 munsell_0.5.0
[103] viridisLite_0.4.1
>
Many thanks Michael! that solved the problem. It's strange how a difference in the packages' version could introduce such an error!