Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this object of class 'GenomicMethylSet'"?
Entering edit mode
maden.sean ▴ 10
Last seen 6 months ago
United States

Hi all,

This is a new error I haven't experienced in eight months working with minfi, until last week. When attempting to load a GenomicMethylSet, either as part of an environment or as an individual .rda file, I receive the following error message: 

Error in nrow(x@elementMetadata) :
  error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: no slot of name "elementMetadata" for this object of class "GenomicMethylSet"

In the following instance, I attempted to load an .Rdata file containing a few additional data frames and a numeric matrix. I am able to load these, but then I receive the error message and the gset does not appear in my working environment. I realize saved .rda and .Rdata files can become corrupted, but it just seems odd to have this error specifically pertaining to the GenomicMethylSet. Haven't seen this issue posted elsewhere, so hoping it is just an end user error :)

Here is my session code as an example ("env_cluster_110515.RData" contains the GenomicMethylSet):

> load("~/dnaarray/env_cluster_110515.RData")
Loading required package: minfi
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append,, as.vector, cbind, colnames,,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax,, pmin,, Position, rank, rbind, Reduce, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages

Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1      2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error in nrow(x@elementMetadata) : 
  error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: no slot of name "elementMetadata" for this object of class "GenomicMethylSet"
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

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

other attached packages:
 [1] minfi_1.16.0               bumphunter_1.10.0          locfit_1.5-9.1            
 [4] iterators_1.0.8            foreach_1.4.3              Biostrings_2.38.0         
 [7] XVector_0.10.0             SummarizedExperiment_1.0.1 GenomicRanges_1.22.1      
[10] GenomeInfoDb_1.6.1         IRanges_2.4.1              S4Vectors_0.8.1           
[13] lattice_0.20-33            Biobase_2.30.0             BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] mclust_5.1              rgl_0.95.1367           base64_1.1             
 [4] Rcpp_0.12.1             Rsamtools_1.22.0        digest_0.6.8           
 [7] plyr_1.8.3              futile.options_1.0.0    ellipse_0.3-8          
[10] RSQLite_1.0.0           ggplot2_1.0.1           zlibbioc_1.16.0        
[13] GenomicFeatures_1.22.4  annotate_1.48.0         preprocessCore_1.32.0  
[16] proto_0.3-10            splines_3.2.2           BiocParallel_1.4.0     
[19] stringr_1.0.0           munsell_0.4.2           igraph_1.0.1           
[22] pheatmap_1.0.7          RCurl_1.95-4.7          biomaRt_2.26.0         
[25] rtracklayer_1.30.1      multtest_2.26.0         pkgmaker_0.22          
[28] GEOquery_2.36.0         quadprog_1.5-5          codetools_0.2-14       
[31] matrixStats_0.15.0      XML_3.98-1.3            reshape_0.8.5          
[34] GenomicAlignments_1.6.1 MASS_7.3-44             bitops_1.0-6           
[37] grid_3.2.2              gtable_0.1.2            nlme_3.1-122           
[40] xtable_1.8-0            registry_0.3            DBI_0.3.1              
[43] magrittr_1.5            scales_0.3.0            stringi_1.0-1          
[46] reshape2_1.4.1          genefilter_1.52.0       doRNG_1.6              
[49] RPMM_1.20               limma_3.26.1            futile.logger_1.4.1    
[52] nor1mix_1.2-1           lambda.r_1.1.7          RColorBrewer_1.1-2     
[55] mixOmics_5.1.2          siggenes_1.44.0         tools_3.2.2            
[58] illuminaio_0.12.0       rngtools_1.2.4          survival_2.38-3        
[61] colorspace_1.2-6        AnnotationDbi_1.32.0    cluster_2.0.3          
[64] beanplot_1.2    


minfi • 1.7k views
Entering edit mode
Last seen 10 weeks ago
United States
GenomicMethylSet builds on a so-called "SummarizedExperiment", a class defined in another package. The authors of SummarizedExperiment recently decided to change the underlying structure of this class. This means that objects created using an old(er) version of minfi/Bioconductor does not work out of the box in new(er) versions of minfi. Usually, you can fix this by doing GMset = updateObject(GMset) (which you can then re-save). If that fails, you may have to re-generate the object from scratch. In my experience, I have always been able to fix it using updateObject(). Best, Kasper
Entering edit mode

Thanks for the reply, Kasper. I will add this step to my workflow.



Entering edit mode

I have the same issue.

I created the object on the server and am now loading it in RStudio.


But apparently your trick won't work, as it won't be loaded at all... Any alternative, other then making the object from scratch...?

Entering edit mode

Please include the result of running sessionInfo() to help diagnose the problem. Does it work if you load the object from command line R rather than from Rstudio? 


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