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Question: DESeq failure after update: unable to find an inherited method for function mcols for signature Rle
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gravatar for ap3637
4 weeks ago by
ap36370
ap36370 wrote:

I'm running DESeq2 and just updated all of my packages.  Now suddenly I can't run several DESeq functions, rlog, varianceStabilizingTransformation, and DESeq functions now all throw this error.  

 

Here is my session info:

 

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.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     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.26.1       ggthemes_3.4.0             tidyr_0.7.2                reshape2_1.4.2             genefilter_1.58.1         
 [6] PoiClaClu_1.0.2            RColorBrewer_1.1-2         pheatmap_1.0.8             ggplot2_2.2.1              DESeq2_1.16.1             
[11] SummarizedExperiment_1.6.5 DelayedArray_0.2.7         matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.6      
[16] GenomeInfoDb_1.12.3        IRanges_2.10.5             S4Vectors_0.14.7           BiocGenerics_0.22.1        devtools_1.13.3           
[21] usethis_0.0.0.9000        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6            bit64_0.9-7             rprojroot_1.2           tools_3.4.0             backports_1.1.1         R6_2.2.2               
 [7] rpart_4.1-11            Hmisc_4.0-3             DBI_0.7                 lazyeval_0.2.0          colorspace_1.3-2        nnet_7.3-12            
[13] ciiDE_1.0.0             withr_2.0.0             gridExtra_2.3           processx_2.0.0.1        bit_1.1-12              compiler_3.4.0         
[19] git2r_0.19.0            htmlTable_1.9           xml2_1.1.1              desc_1.1.1              scales_0.5.0            checkmate_1.8.4        
[25] callr_1.0.0             commonmark_1.4          stringr_1.2.0           digest_0.6.12           foreign_0.8-69          XVector_0.16.0         
[31] base64enc_0.1-3         htmltools_0.3.6         htmlwidgets_0.9         rlang_0.1.2             rstudioapi_0.7          RSQLite_2.0            
[37] BiocParallel_1.10.1     acepack_1.4.1           RCurl_1.95-4.8          magrittr_1.5            GenomeInfoDbData_0.99.0 Formula_1.2-2          
[43] Matrix_1.2-11           Rcpp_0.12.13            munsell_0.4.3           stringi_1.1.5           debugme_1.0.2           zlibbioc_1.22.0        
[49] pkgbuild_0.0.0.9000     plyr_1.8.4              grid_3.4.0              blob_1.1.0              crayon_1.3.4            lattice_0.20-35        
[55] splines_3.4.0           annotate_1.54.0         locfit_1.5-9.1          knitr_1.17              geneplotter_1.54.0      clisymbols_1.2.0       
[61] pkgload_0.0.0.9000      XML_3.98-1.9            glue_1.1.1              latticeExtra_0.6-28     data.table_1.10.4-2     gtable_0.2.0           
[67] purrr_0.2.3             assertthat_0.2.0        xtable_1.8-2            roxygen2_6.0.1          survival_2.41-3         tibble_1.3.4           
[73] AnnotationDbi_1.38.2    memoise_1.1.0           cluster_2.0.6          

 

> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).

 

> library(BiocInstaller)
> biocValid()  
[1] TRUE

 

Here is my making my data object and producing the error:

dds <- DESeqDataSetFromMatrix(countData = count_data, colData = target_data, design = ~Treatment_Time)

dds <- estimateSizeFactors(dds)

> dds
class: DESeqDataSet 
dim: 58233 313 
metadata(1): version
assays(1): counts
rownames(58233): ENSG00000127720 ENSG00000275852 ... ENSG00000119509 ENSG00000200487
rowData names(0):
colnames(313): JUL_0001_rep1_patient1_day3_Flucelvax_Influenza_Male_Age30_batch1
  JUL_0001_rep2_patient1_day3_Flucelvax_Influenza_Male_Age30_batch1 ... JUL_0127_rep2_patient45_day3_Flucelvax_Influenza_Male_Age19_batch12
  JUL_0127_rep3_patient45_day3_Flucelvax_Influenza_Male_Age19_batch12
colData names(21): Unique.ID LongName ... Treatment_Sex_Time sizeFactor

 

Now here is the error:

> rld <- rlog(dds)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘mcols’ for signature ‘"Rle"’

Same with variance stabilizing:

> rld <- varianceStabilizingTransformation(dds)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘mcols’ for signature ‘"Rle"’

Same for DESeq

> DESeq(dds)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘mcols’ for signature ‘"Rle"’

 

Also here is my showMethods(mcols)

> showMethods(mcols)
Function: mcols (package S4Vectors)
x="DataFrame"
    (inherited from: x="Vector")
x="DESeqDataSet"
    (inherited from: x="RangedSummarizedExperiment")
x="GRanges"
    (inherited from: x="Vector")
x="GRangesList"
    (inherited from: x="Vector")
x="IRanges"
    (inherited from: x="Vector")
x="RangedSummarizedExperiment"
x="SummarizedExperiment"
    (inherited from: x="Vector")
x="Vector"

 

I'm having trouble finding any information about this on the web and am not sure exactly what the issue is.  I would appreciate any advice anyone can offer.  Thanks in advance.

ADD COMMENTlink modified 4 weeks ago by Michael Love14k • written 4 weeks ago by ap36370
0
gravatar for Michael Love
4 weeks ago by
Michael Love14k
United States
Michael Love14k wrote:

This is a strange error. What do you get with mcols(dds)

ADD COMMENTlink written 4 weeks ago by Michael Love14k

I just tried updating all packages and I don't throw an error:

> dds <- makeExampleDESeqDataSet()
> dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).
> biocValid()
[1] TRUE
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

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 datasets  utils    
[8] methods   base     

other attached packages:
 [1] DESeq2_1.16.1              SummarizedExperiment_1.6.5
 [3] DelayedArray_0.2.7         matrixStats_0.52.2        
 [5] Biobase_2.36.2             GenomicRanges_1.28.6      
 [7] GenomeInfoDb_1.12.3        IRanges_2.10.5            
 [9] S4Vectors_0.14.7           BiocGenerics_0.22.1       
[11] BiocInstaller_1.26.1       rmarkdown_1.6             
[13] testthat_1.0.2             devtools_1.13.3           

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1          Rcpp_0.12.13            lattice_0.20-35        
 [4] rprojroot_1.2           digest_0.6.12           R6_2.2.2               
 [7] plyr_1.8.4              backports_1.1.1         acepack_1.4.1          
[10] RSQLite_2.0             evaluate_0.10.1         ggplot2_2.2.1          
[13] zlibbioc_1.22.0         rlang_0.1.2             lazyeval_0.2.0         
[16] rstudioapi_0.7          data.table_1.10.4-2     annotate_1.54.0        
[19] blob_1.1.0              rpart_4.1-11            Matrix_1.2-11          
[22] checkmate_1.8.4         splines_3.4.0           BiocParallel_1.10.1    
[25] geneplotter_1.54.0      stringr_1.2.0           foreign_0.8-69         
[28] htmlwidgets_0.9         bit_1.1-12              RCurl_1.95-4.8         
[31] munsell_0.4.3           compiler_3.4.0          base64enc_0.1-3        
[34] htmltools_0.3.6         nnet_7.3-12             tibble_1.3.4           
[37] gridExtra_2.3           htmlTable_1.9           GenomeInfoDbData_0.99.0
[40] Hmisc_4.0-3             XML_3.98-1.9            crayon_1.3.4           
[43] withr_2.0.0             bitops_1.0-6            grid_3.4.0             
[46] xtable_1.8-2            gtable_0.2.0            DBI_0.7                
[49] magrittr_1.5            scales_0.5.0            stringi_1.1.5          
[52] XVector_0.16.0          genefilter_1.58.1       latticeExtra_0.6-28    
[55] Formula_1.2-2           RColorBrewer_1.1-2      tools_3.4.0            
[58] bit64_0.9-7             survival_2.41-3         AnnotationDbi_1.38.2   
[61] colorspace_1.3-2        cluster_2.0.6           memoise_1.1.0          
[64] knitr_1.17   
ADD REPLYlink written 4 weeks ago by Michael Love14k

I get the following.  Shows 0 columns when i do this, but the dds shows 313.   This is really strange.

> mcols(dds)
DataFrame with 58233 rows and 0 columns
ADD REPLYlink written 4 weeks ago by ap36370

I seem to have resolved it, though I'm not sure exactly why.

I updated devtools and roxygen packages and it seems to work again for some reason.  

ADD REPLYlink written 4 weeks ago by ap36370
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