Question: DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
0
gravatar for 200dumplings
4 weeks ago by
200dumplings0 wrote:

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?

ADD COMMENTlink modified 4 weeks ago by Martin Morgan ♦♦ 23k • written 4 weeks ago by 200dumplings0
Answer: DESeq2: Null Pointer Object when building dds S4 object
0
gravatar for Michael Love
4 weeks ago by
Michael Love24k
United States
Michael Love24k wrote:

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

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Michael Love24k

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

ADD REPLYlink written 4 weeks ago by 200dumplings0

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

ADD REPLYlink written 4 weeks ago by Michael Love24k

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?

ADD REPLYlink written 4 weeks ago by Michael Love24k

I updated my answer

ADD REPLYlink written 4 weeks ago by Michael Love24k

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!

ADD REPLYlink written 28 days ago by 200dumplings0
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