DESeqDataSetFromMatrix {DESeq2} is wrong on my computer
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Entering edit mode
zxy5139 • 0
@zxy5139-13559
Last seen 7.4 years ago

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DESeq2_1.16.1              SummarizedExperiment_1.4.0 Biobase_2.34.0             GenomicRanges_1.26.3      
[5] GenomeInfoDb_1.10.3        IRanges_2.8.1              S4Vectors_0.12.0           BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] genefilter_1.56.0    locfit_1.5-9.1       splines_3.4.0        lattice_0.20-35      colorspace_1.3-2    
 [6] htmltools_0.3.6      base64enc_0.1-3      blob_1.1.0           survival_2.41-3      XML_3.98-1.9        
[11] rlang_0.1.1          foreign_0.8-69       DBI_0.7              BiocParallel_1.8.2   bit64_0.9-7         
[16] RColorBrewer_1.1-2   matrixStats_0.52.2   plyr_1.8.4           stringr_1.2.0        zlibbioc_1.20.0     
[21] munsell_0.4.3        gtable_0.2.0         htmlwidgets_0.9      memoise_1.1.0        latticeExtra_0.6-28 
[26] knitr_1.16           geneplotter_1.52.0   AnnotationDbi_1.36.2 htmlTable_1.9        Rcpp_0.12.12        
[31] acepack_1.4.1        xtable_1.8-2         scales_0.4.1         backports_1.1.0      checkmate_1.8.3     
[36] DelayedArray_0.3.16  Hmisc_4.0-3          annotate_1.52.1      XVector_0.14.0       bit_1.1-12          
[41] gridExtra_2.2.1      ggplot2_2.2.1        digest_0.6.12        stringi_1.1.5        grid_3.4.0          
[46] bitops_1.0-6         tools_3.4.0          magrittr_1.5         lazyeval_0.2.0       RCurl_1.95-4.8      
[51] tibble_1.3.3         RSQLite_2.0          Formula_1.2-2        cluster_2.0.6        Matrix_1.2-10       
[56] data.table_1.10.4    rpart_4.1-11         nnet_7.3-12          compiler_3.4.0      

 

> countData <- matrix(1:100,ncol=4)
> condition <- factor(c("A","A","B","B"))
> dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~ condition)
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class “NULL” is not valid for slot ‘NAMES’ in an object of class “DESeqDataSet”; is(value, "character_OR_NULL") is not TRUE

 

 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("DelayedArray")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘DelayedArray’
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4:
  can not open URL'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4:
  can not open URL'https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4:
  can not open URL'https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4/PACKAGES'
Old packages: 'AnnotationHub', 'curl', 'fgsea', 'GenomicAlignments', 'GenomicRanges', 'GOSemSim', 'IRanges', 'limma', 'Rsamtools', 'S4Vectors',
  'VariantAnnotation', 'XVector'
Update all/some/none? [a/s/n]:

 

can anyone know the reason why DESeqDataSetFromMatrix {DESeq2}  is wrong and I can not install  DelayedArray package??

 

 

 

deseq2 DESeqDataSetFromMatrix • 1.8k views
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0
Entering edit mode
@mikelove
Last seen 1 day ago
United States

You have a mix of current and out of date Bioc packages. Try updating all with biocLite() and then restart R. This usually fixes things.

 

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0
Entering edit mode

I have tried what you said, but there is another question?

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 
  missing value where TRUE/FALSE needed 

I think something about the version of R or bioconductor is wrong.

I have just tried edgeR today with R 3.4.0 successfully, so I will choose edgeR for bioinformatics.Thanks a lot for your answer.

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1
Entering edit mode

That's fine :)

If you continue to have problems installing Bioc packages, you can post this latest error and get some help. Usually the issue is that Bioc packages were installed in multiple locations or not using biocLite.

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