Question: Recurring error in smoothMethygenoset step for MethyAnalysis
0
gravatar for charleneee95
21 months ago by
charleneee950 wrote:

Dear all,

I have been trying to run methyAnalysis on my methylation data and have gotten past the step of creating the Methygenoset.

I created the Methygenoset using the command below:

> Methygenoset <- MethyGenoSet(rowRanges = gr, methylated = CG.signals.meth, unmethylated = CG.signals.unmeth, detection = pvalue, exprs = CG.beta.matrix, pData = phenoData)

Details of the Methygenoset are here. 

> Methygenoset
class: MethyGenoSet 
dim: 474517 12 
metadata(0):
assays(4): exprs methylated unmethylated detecton
rownames(474517): cg00000029 cg00000108 ...
  ch.X.97737721F ch.X.98007042R
rowData names(0):
colnames(12): CRO.AP.2 FARAGE ... SU.DHL.4 WSU.DLCL2
colData names(1): Type

Nevertheless, at the smoothing step, I encountered an error that I have no idea how to fix. The code i used at the smoothing step is the same as that written in the methyAnalysis vignette. However, this is the output I received:

> Methygenoset.sm <- smoothMethyData(Methygenoset, winSize = 250)
Smoothing Chromosome chr1 ...
Smoothing Chromosome chr10 ...
Smoothing Chromosome chr11 ...
Smoothing Chromosome chr12 ...
Smoothing Chromosome chr13 ...
Smoothing Chromosome chr14 ...
Smoothing Chromosome chr15 ...
Smoothing Chromosome chr16 ...
Smoothing Chromosome chr17 ...
Smoothing Chromosome chr18 ...
Smoothing Chromosome chr19 ...
Smoothing Chromosome chr2 ...
Smoothing Chromosome chr20 ...
Smoothing Chromosome chr21 ...
Smoothing Chromosome chr22 ...
Smoothing Chromosome chr3 ...
Smoothing Chromosome chr4 ...
Smoothing Chromosome chr5 ...
Smoothing Chromosome chr6 ...
Smoothing Chromosome chr7 ...
Smoothing Chromosome chr8 ...
Smoothing Chromosome chr9 ...
Smoothing Chromosome chrX ...
Smoothing Chromosome chrY ...
Error in `assays<-`(`*tmp*`, value = <S4 object of class "SimpleList">) : 
  current and replacement dimnames() differ

The traceback shows this:

6.
stop("current and replacement dimnames() differ")
5.
`assays<-`(`*tmp*`, value = <S4 object of class structure("SimpleList", package = "S4Vectors")>)
4.
`assays<-`(`*tmp*`, value = <S4 object of class structure("SimpleList", package = "S4Vectors")>)
3.
`exprs<-`(`*tmp*`, value = structure(c(0.880207189957285, 0.939786568719977, 0.523736977897769, 0.523736977897769, 0.523736977897769, 0.855691670400128, 0.901939284129203, 0.0214381149034374, 0.784356105892621, 0.122348363383495, 0.108999417491079, 0.102686909393653, 0.0991019133151113, 0.144419524679435, ...
2.
`exprs<-`(`*tmp*`, value = structure(c(0.880207189957285, 0.939786568719977, 0.523736977897769, 0.523736977897769, 0.523736977897769, 0.855691670400128, 0.901939284129203, 0.0214381149034374, 0.784356105892621, 0.122348363383495, 0.108999417491079, 0.102686909393653, 0.0991019133151113, 0.144419524679435, ... at

<tmp>#85
1.
smoothMethyData(Methygenoset, winSize = 250)

 

I am able to run the smoothMethydata function on the exampleMethygenoset. I have checked and ensured that my Methygenoset is as similar to the exampleMethygenoset that can be found in the package. Please help me in figuring out where the problem is.

Thank you!

My sessioninfo are as follows:

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_SG.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_SG.UTF-8        LC_COLLATE=en_SG.UTF-8    
 [5] LC_MONETARY=en_SG.UTF-8    LC_MESSAGES=en_SG.UTF-8   
 [7] LC_PAPER=en_SG.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_SG.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] compare_0.2-6              BiocInstaller_1.28.0      
 [3] genoset_1.34.0             SummarizedExperiment_1.8.0
 [5] DelayedArray_0.4.1         matrixStats_0.52.2        
 [7] readr_1.1.1                methyAnalysis_1.20.0      
 [9] org.Hs.eg.db_3.5.0         AnnotationDbi_1.40.0      
[11] Biobase_2.38.0             GenomicRanges_1.30.0      
[13] GenomeInfoDb_1.14.0        IRanges_2.12.0            
[15] S4Vectors_0.16.0           BiocGenerics_0.24.0       

loaded via a namespace (and not attached):
  [1] backports_1.1.1               Hmisc_4.0-3                  
  [3] AnnotationHub_2.10.1          plyr_1.8.4                   
  [5] lazyeval_0.2.1                splines_3.4.2                
  [7] BiocParallel_1.12.0           ggplot2_2.2.1                
  [9] digest_0.6.12                 foreach_1.4.3                
 [11] ensembldb_2.2.0               htmltools_0.3.6              
 [13] magrittr_1.5                  checkmate_1.8.5              
 [15] memoise_1.1.0                 BSgenome_1.46.0              
 [17] cluster_2.0.6                 limma_3.34.1                 
 [19] Biostrings_2.46.0             annotate_1.56.1              
 [21] siggenes_1.52.0               prettyunits_1.0.2            
 [23] colorspace_1.3-2              blob_1.1.0                   
 [25] dplyr_0.7.4                   RCurl_1.95-4.8               
 [27] genefilter_1.60.0             bindr_0.1                    
 [29] GEOquery_2.46.9               survival_2.41-3              
 [31] VariantAnnotation_1.24.1      iterators_1.0.8              
 [33] glue_1.2.0                    registry_0.3                 
 [35] gtable_0.2.0                  lumi_2.30.0                  
 [37] zlibbioc_1.24.0               XVector_0.18.0               
 [39] scales_0.5.0                  DBI_0.7                      
 [41] rngtools_1.2.4                Rcpp_0.12.13                 
 [43] xtable_1.8-2                  progress_1.1.2               
 [45] htmlTable_1.9                 bumphunter_1.20.0            
 [47] foreign_0.8-69                bit_1.1-12                   
 [49] mclust_5.4                    preprocessCore_1.40.0        
 [51] Formula_1.2-2                 htmlwidgets_0.9              
 [53] httr_1.3.1                    RColorBrewer_1.1-2           
 [55] acepack_1.4.1                 pkgconfig_2.0.1              
 [57] reshape_0.8.7                 XML_3.98-1.9                 
 [59] Gviz_1.22.0                   nnet_7.3-12                  
 [61] locfit_1.5-9.1                rlang_0.1.4                  
 [63] munsell_0.4.3                 tools_3.4.2                  
 [65] RSQLite_2.0                   stringr_1.2.0                
 [67] yaml_2.1.14                   knitr_1.17                   
 [69] bit64_0.9-7                   beanplot_1.2                 
 [71] methylumi_2.24.1              purrr_0.2.4                  
 [73] AnnotationFilter_1.2.0        bindrcpp_0.2                 
 [75] nlme_3.1-131                  doRNG_1.6.6                  
 [77] mime_0.5                      nor1mix_1.2-3                
 [79] xml2_1.1.1                    biomaRt_2.34.0               
 [81] compiler_3.4.2                curl_3.0                     
 [83] interactiveDisplayBase_1.16.0 affyio_1.48.0                
 [85] tibble_1.3.4                  stringi_1.1.6                
 [87] GenomicFeatures_1.30.0        minfi_1.24.0                 
 [89] lattice_0.20-35               ProtGenerics_1.10.0          
 [91] Matrix_1.2-12                 multtest_2.34.0              
 [93] data.table_1.10.4-3           bitops_1.0-6                 
 [95] httpuv_1.3.5                  rtracklayer_1.38.0           
 [97] R6_2.2.2                      latticeExtra_0.6-28          
 [99] affy_1.56.0                   RMySQL_0.10.13               
[101] KernSmooth_2.23-15            gridExtra_2.3                
[103] nleqslv_3.3.1                 codetools_0.2-15             
[105] dichromat_2.0-0               MASS_7.3-47                  
[107] assertthat_0.2.0              openssl_0.9.9                
[109] pkgmaker_0.22                 GenomicAlignments_1.14.1     
[111] Rsamtools_1.30.0              GenomeInfoDbData_0.99.1      
[113] mgcv_1.8-22                   hms_0.4.0                    
[115] quadprog_1.5-5                rpart_4.1-11                 
[117] tidyr_0.7.2                   base64_2.0                   
[119] illuminaio_0.20.0             biovizBase_1.26.0            
[121] shiny_1.0.5                   base64enc_0.1-3      
methyanalysis • 324 views
ADD COMMENTlink written 21 months ago by charleneee950
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