Question: DESeq2/SummarizedExperiment RStudio shows Object With Null Pointer
0
gravatar for 200dumplings
4 months 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 months ago by Martin Morgan ♦♦ 24k • written 4 months ago by 200dumplings0
Answer: DESeq2: Null Pointer Object when building dds S4 object
0
gravatar for Michael Love
4 months ago by
Michael Love26k
United States
Michael Love26k 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 months ago • written 4 months ago by Michael Love26k

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

ADD REPLYlink written 4 months ago by 200dumplings0

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

ADD REPLYlink written 4 months ago by Michael Love26k

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 months ago by Michael Love26k

I updated my answer

ADD REPLYlink written 4 months ago by Michael Love26k

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 4 months ago by 200dumplings0

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

ADD REPLYlink written 3 months ago by aless910

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by Michael Love26k
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