Minfi read.metharray error in checkslotassignment
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Entering edit mode
lily • 0
@lily-11487
Last seen 5.1 years ago

I am running a set of analyses in Minfi. I have previously used Minfi with a different dataset, and it ran smoothly. However, this time I am getting the following error after inputting the data (in this new round I have idat files with different array sizes, so used the force=TRUE)

library(minfi)
targetsNsg <- read.metharray.sheet("minfi")
RGsetNsg <- read.metharray.exp(targets=targetsNsg, force=TRUE)

Error in checkSlotAssignment(object, name, value) : 

  assignment of an object of class “character” is not valid for slot ‘NAMES’ in an object of class “RGChannelSet”; is(value, "character_OR_NULL") is not TRUE

If you could please let me know if you have a solution for this error, it would be greatly appreciated.

 

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] RnBeads_1.6.1                          
 [2] plyr_1.8.4                             
 [3] methylumi_2.20.0                       
 [4] minfi_1.22.1                           
 [5] bumphunter_1.14.0                      
 [6] locfit_1.5-9.1                         
 [7] iterators_1.0.8                        
 [8] foreach_1.4.3                          
 [9] Biostrings_2.41.4                      
[10] XVector_0.13.7                         
[11] SummarizedExperiment_1.3.82            
[12] FDb.InfiniumMethylation.hg19_2.2.0     
[13] org.Hs.eg.db_3.4.0                     
[14] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[15] GenomicFeatures_1.26.4                 
[16] AnnotationDbi_1.36.2                   
[17] reshape2_1.4.2                         
[18] scales_0.5.0                           
[19] Biobase_2.33.3                         
[20] illuminaio_0.16.0                      
[21] matrixStats_0.52.2                     
[22] limma_3.30.13                          
[23] gridExtra_2.2.1                        
[24] gplots_3.0.1                           
[25] ggplot2_2.2.1                          
[26] fields_9.0                             
[27] maps_3.2.0                             
[28] spam_2.1-1                             
[29] dotCall64_0.9-04                       
[30] ff_2.2-13                              
[31] bit_1.1-12                             
[32] cluster_2.0.6                          
[33] RColorBrewer_1.1-2                     
[34] MASS_7.3-47                            
[35] GenomicRanges_1.25.94                  
[36] GenomeInfoDb_1.9.12                    
[37] IRanges_2.7.15                         
[38] S4Vectors_0.11.14                      
[39] BiocGenerics_0.19.2                    

loaded via a namespace (and not attached):
 [1] nlme_3.1-131             bitops_1.0-6            
 [3] bit64_0.9-7              httr_1.3.1              
 [5] tools_3.4.1              doRNG_1.6.6             
 [7] nor1mix_1.2-3            R6_2.2.2                
 [9] KernSmooth_2.23-15       DBI_0.7                 
[11] lazyeval_0.2.0           colorspace_1.3-2        
[13] base64_2.0               compiler_3.4.1          
[15] preprocessCore_1.36.0    pkgmaker_0.22           
[17] rtracklayer_1.34.2       caTools_1.17.1          
[19] quadprog_1.5-5           genefilter_1.56.0       
[21] stringr_1.2.0            digest_0.6.12           
[23] Rsamtools_1.26.2         siggenes_1.48.0         
[25] GEOquery_2.40.0          pkgconfig_2.0.1         
[27] rlang_0.1.2              RSQLite_2.0             
[29] mclust_5.3               BiocParallel_1.8.2      
[31] gtools_3.5.0             RCurl_1.95-4.8          
[33] magrittr_1.5             Matrix_1.2-10           
[35] Rcpp_0.12.12             munsell_0.4.3           
[37] stringi_1.1.5            zlibbioc_1.20.0         
[39] blob_1.1.0               gdata_2.18.0            
[41] lattice_0.20-35          splines_3.4.1           
[43] annotate_1.52.1          multtest_2.30.0         
[45] beanplot_1.2             rngtools_1.2.4          
[47] codetools_0.2-15         biomaRt_2.30.0          
[49] XML_3.98-1.9             data.table_1.10.4       
[51] gtable_0.2.0             openssl_0.9.6           
[53] reshape_0.8.7            xtable_1.8-2            
[55] survival_2.41-3          tibble_1.3.4            
[57] GenomicAlignments_1.10.1 registry_0.3            
[59] memoise_1.1.0  

minfi read.metharray.exp • 1.1k views
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Entering edit mode
mcastrod • 0
@mcastrod-10187
Last seen 4.0 years ago

Hi,

Did you find a solution for this issue? I got the same error after upgrading R to 3.4.3 and minfi to 1.28. I tried with older versions and I have the same error with EPIC and 450k arrays. The only strange thing is two missing file link warnings during minfi installation but there was no error. 

Thanks!

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Entering edit mode

Have you checked whether your system is current by running 

biocValid()

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