Error in SummarizedExperiment in DESeq2
1
0
Entering edit mode
Cherif • 0
@64f6927a
Last seen 5 weeks ago
United Kingdom

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          
>
DESeq2 • 167 views
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1
Entering edit mode
@mikelove
Last seen 5 hours ago
United States

This is a helpful check. It's actually coming from SummarizedExperiment, not DESeq2.

It says you have provided mismatching information on the columns of counts and the rows of the colData. These should be matching.

If you are certain they are aligned, but just have different names (be careful), you can remove colnames of the counts and the error will go away. colnames(counts) <- NULL

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Entering edit mode

Many thanks Michael! that solved the problem. It's strange how a difference in the packages' version could introduce such an error!

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