Question: Error creating DESeqDataSet from "airway" SummarizedExperiment
0
gravatar for Levi Waldron
2.5 years ago by
Levi Waldron980
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron980 wrote:

Trying to run the "airway" RNA-seq workflow, I get an error when creating the the DESeqDataSet, on both release and devel (example from release below). It seems to be related to the renaming of GenomicRangesORGRangesList to GenomicRanges_OR_GRangesList:

> suppressPackageStartupMessages(library(DESeq2))
> library(airway)
> data("airway")
> dds <- DESeqDataSet(airway, design = ~cell + dex)
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “DESeqDataSet”; is(value, "GenomicRangesORGRangesList") is not TRUE
> is(rowRanges(airway))
[1] "GRangesList"                  "CompressedList"              
[3] "GenomicRangesList"            "GenomicRanges_OR_GRangesList"
[5] "List"                         "Vector"                      
[7] "Annotated"                   
> sessionInfo()
R version 3.4.0 Patched (2017-06-02 r72758)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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    
[7] datasets  methods   base     

other attached packages:
 [1] airway_0.111.0             DESeq2_1.17.3             
 [3] SummarizedExperiment_1.7.5 DelayedArray_0.3.16       
 [5] matrixStats_0.52.2         Biobase_2.37.2            
 [7] GenomicRanges_1.29.6       GenomeInfoDb_1.13.4       
 [9] IRanges_2.11.5             S4Vectors_0.15.4          
[11] BiocGenerics_0.23.0       

loaded via a namespace (and not attached):
 [1] genefilter_1.59.0       locfit_1.5-9.1         
 [3] splines_3.4.0           lattice_0.20-35        
 [5] colorspace_1.3-2        htmltools_0.3.6        
 [7] base64enc_0.1-3         blob_1.1.0             
 [9] survival_2.41-3         XML_3.98-1.9           
[11] rlang_0.1.1             DBI_0.7                
[13] foreign_0.8-69          BiocParallel_1.11.2    
[15] bit64_0.9-7             RColorBrewer_1.1-2     
[17] GenomeInfoDbData_0.99.1 plyr_1.8.4             
[19] stringr_1.2.0           zlibbioc_1.23.0        
[21] munsell_0.4.3           gtable_0.2.0           
[23] htmlwidgets_0.8         memoise_1.1.0          
[25] latticeExtra_0.6-28     knitr_1.16             
[27] geneplotter_1.55.0      AnnotationDbi_1.39.1   
[29] htmlTable_1.9           Rcpp_0.12.11           
[31] acepack_1.4.1           xtable_1.8-2           
[33] scales_0.4.1            backports_1.1.0        
[35] checkmate_1.8.2         Hmisc_4.0-3            
[37] annotate_1.55.0         XVector_0.17.0         
[39] bit_1.1-12              gridExtra_2.2.1        
[41] ggplot2_2.2.1           digest_0.6.12          
[43] stringi_1.1.5           grid_3.4.0             
[45] tools_3.4.0             bitops_1.0-6           
[47] magrittr_1.5            RSQLite_2.0            
[49] lazyeval_0.2.0          RCurl_1.95-4.8         
[51] tibble_1.3.3            Formula_1.2-1          
[53] cluster_2.0.6           Matrix_1.2-10          
[55] data.table_1.10.4       rpart_4.1-11           
[57] nnet_7.3-12             compiler_3.4.0     

> 

 

genomicranges deseq2 • 1.5k views
ADD COMMENTlink modified 2.5 years ago by Hervé Pagès ♦♦ 14k • written 2.5 years ago by Levi Waldron980

BTW, updateObject(airway) does something, but doesn't actually let me create a DESeqDataSet:

> is(rowRanges(updateObject(airway)))
[1] "GRangesList"                 
[2] "CompressedList"              
[3] "GenomicRangesList"           
[4] "GenomicRanges_OR_GRangesList"
[5] "List"                        
[6] "Vector"                      
[7] "Annotated"                   
> dds <- DESeqDataSet(updateObject(airway), design = ~cell + dex)
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “DESeqDataSet”; is(value, "GenomicRangesORGRangesList") is not TRUE
> 
ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Levi Waldron980
Answer: Error creating DESeqDataSet from "airway" SummarizedExperiment
1
gravatar for Martin Morgan
2.5 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Try re-installing DESeq2; it seems like there is a stale cached class definition.

ADD COMMENTlink written 2.5 years ago by Martin Morgan ♦♦ 24k

Thanks Martin, that did the trick (installing from source):

> biocLite("DESeq2", type="source")
ADD REPLYlink written 2.5 years ago by Levi Waldron980
Answer: Error creating DESeqDataSet from "airway" SummarizedExperiment
0
gravatar for Hervé Pagès
2.5 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi Levi,

Thanks for reporting this. I'll bump DESeq2's version and also the version of other packages that define RangedSummarizedExperiment derivatives. This will help getting rid of the stale class definitions that are cached on the user machines.

BTW are you sure you also got this problem in release? I only renamed GenomicRangesORGRangesList -> GenomicRanges_OR_GRangesList in devel (in GenomicRanges 1.29.6 to be precised) so I'm surprised that this also affects release.

Thanks,

H.

ADD COMMENTlink written 2.5 years ago by Hervé Pagès ♦♦ 14k

This is done. I bumped the version for 19 packages in devel. Actually didn't need to do it for DESeq2 (Mike did it yesterday).

Cheers,

H.

ADD REPLYlink written 2.5 years ago by Hervé Pagès ♦♦ 14k
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