Minfi read.metharray error in checkslotassignment
4
0
Entering edit mode
lily • 0
@lily-11487
Last seen 6.5 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 • 1.4k views
ADD COMMENT
0
Entering edit mode
mcastrod • 0
@mcastrod-10187
Last seen 5.5 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!

ADD COMMENT
0
Entering edit mode

Have you checked whether your system is current by running 

biocValid()

ADD REPLY

Login before adding your answer.

Traffic: 891 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6