DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
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@200dumplings-21103
Last seen 2.2 years ago

I have been failing to build a DDS object using the function DESeqDataSetFromMatrix()

Here is some randomly generated matrix I am using to test out if my DEseq2 package is working properly:

x <- round(matrix(rexp(480 * 10, rate=.1), ncol=12), 0)
rownames(x) <- paste("gene", 1:nrow(x))
colnames(x) <- paste("sample", 1:ncol(x))

coldata <- data.frame(condition = factor(c(rep("ctl", 3), rep("A", 3), rep("B", 3), rep("C", 3))))

coldata$condition <- relevel(coldata$condition, ref = "ctl")

library(DESeq2)
dds <- DESeqDataSetFromMatrix(countData = x, colData = coldata, design= ~ condition)

The dds object shows up as <object with="" null="" pointer="">

Here is my SessionInfo()

> R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.24.0               SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
 [4] BiocParallel_1.18.0         matrixStats_0.54.0          Biobase_2.44.0             
 [7] GenomicRanges_1.36.0        GenomeInfoDb_1.20.0         IRanges_2.18.1             
[10] S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1             locfit_1.5-9.1         lattice_0.20-38       
 [4] assertthat_0.2.1       digest_0.6.19          R6_2.4.0              
 [7] backports_1.1.4        acepack_1.4.1          RSQLite_2.1.1         
[10] ggplot2_3.2.0          pillar_1.4.1           zlibbioc_1.30.0       
[13] rlang_0.3.4            lazyeval_0.2.2         annotate_1.62.0       
[16] rstudioapi_0.10        data.table_1.12.2      blob_1.1.1            
[19] rpart_4.1-15           Matrix_1.2-17          checkmate_1.9.3       
[22] splines_3.6.0          geneplotter_1.62.0     stringr_1.4.0         
[25] foreign_0.8-71         htmlwidgets_1.3        bit_1.1-14            
[28] RCurl_1.95-4.12        munsell_0.5.0          compiler_3.6.0        
[31] xfun_0.7               pkgconfig_2.0.2        base64enc_0.1-3       
[34] htmltools_0.3.6        nnet_7.3-12            tidyselect_0.2.5      
[37] tibble_2.1.3           gridExtra_2.3          htmlTable_1.13.1      
[40] GenomeInfoDbData_1.2.1 Hmisc_4.2-0            XML_3.98-1.20         
[43] crayon_1.3.4           dplyr_0.8.1            bitops_1.0-6          
[46] grid_3.6.0             DBI_1.0.0              xtable_1.8-4          
[49] gtable_0.3.0           magrittr_1.5           scales_1.0.0          
[52] stringi_1.4.3          XVector_0.24.0         genefilter_1.66.0     
[55] latticeExtra_0.6-28    Formula_1.2-3          RColorBrewer_1.1-2    
[58] tools_3.6.0            bit64_0.9-7            glue_1.3.1            
[61] purrr_0.3.2            survival_2.44-1.1      AnnotationDbi_1.46.0  
[64] colorspace_1.4-1       cluster_2.1.0          BiocManager_1.30.4    
[67] memoise_1.1.0          knitr_1.23

I have tried to uninstall the DESeq2 and SummarisedExperiment packages, and reinstalled them, but still cannot build a proper object.

Can someone tell me what is broken?

deseq2 null summarizedexperiment rstudio • 1.6k views
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1
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@mikelove
Last seen 7 hours ago
United States

Updated answer:

This is not an R or Bioconductor bug. It’s just an “artifact” from RStudio’s interface. There is nothing wrong and you can use your Bioconductor packages while ignoring this “artifact” of what it shows in the Environment pane.

See here:

https://github.com/rstudio/rstudio/issues/4741

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0
Entering edit mode

Hi Michael, BiocManager::valid("DESeq2") returns TRUE. I have only encountered this problem after the R and RStudio update.

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0
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Can you run valid()? It needs to check all packages.

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Another question, can you type

dds 

Into the console after? What do you mean when you say “it shows up as...” do you mean in RStudio’s environment panel, or in the R console?

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I updated my answer

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Thank you Michael! I think the object is there and is not null. Here is the output when I run

dds

class: DESeqDataSet dim: 46078 12 metadata(1): version assays(1): counts rownames(46078): ENSMUSG00000028180 ENSMUSG00000028182 ... ENSMUSG00000036958 ENSMUSG00000042678 rowData names(0): colnames(12): ctrl1 group11 ... group23 group33 colData names(1): condition

Resolved so far!

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A part from dds object shows up as <object with="" null="" pointer="">, when typing dds I get also Warning messages: 1: In class(object) <- "environment" : Setting class(x) to "environment" sets attribute to NULL; result will no longer be an S4 object Can I ignore it? thank you

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See the answer above.

This piece of information in the RStudio Environment panel contains no useful information about the Bioc objects and can be ignored.

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