Hi,

I would like to analyse some Illumima 450K methylation bead arrays. Using the mapToGenome() function I encountered an error, which occurs even with the example code of the documentation.

Has anyone encountered such an error ?

Thanks in advance.

Cathy.

> library("minfi")
> ?mapToGenome
> if (require(minfiData)) {
+        ## MsetEx.sub is a small subset of MsetEx;
+        ## only used for computational speed.
+        GMsetEx.sub <- mapToGenome(MsetEx.sub)
+      }
Error in as.vector(x, mode) :
  '.SigArgs' is shorter than '.SigLength' says it should be
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

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

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

other attached packages:
 [1] BiocInstaller_1.24.0                              
 [2] minfiData_0.20.0                                  
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
 [4] IlluminaHumanMethylation450kmanifest_0.4.0        
 [5] minfi_1.20.2                                      
 [6] bumphunter_1.14.0                                 
 [7] locfit_1.5-9.1                                    
 [8] iterators_1.0.8                                   
 [9] foreach_1.4.3                                     
[10] Biostrings_2.42.1                                 
[11] XVector_0.14.1                                    
[12] SummarizedExperiment_1.4.0                        
[13] Biobase_2.34.0                                    
[14] GenomicRanges_1.26.4                              
[15] GenomeInfoDb_1.10.3                               
[16] IRanges_2.8.2                                     
[17] S4Vectors_0.12.2                                  
[18] BiocGenerics_0.20.0                               

loaded via a namespace (and not attached):
 [1] mclust_5.2.3             base64_2.0               Rcpp_0.12.10            
 [4] lattice_0.20-24          Rsamtools_1.26.1         digest_0.6.12           
 [7] R6_2.2.0                 plyr_1.8.4               RSQLite_1.1-2           
[10] httr_1.2.1               zlibbioc_1.20.0          GenomicFeatures_1.26.3  
[13] data.table_1.10.4        annotate_1.52.1          Matrix_1.1-2            
[16] preprocessCore_1.36.0    splines_3.3.1            BiocParallel_1.8.1      
[19] stringr_1.2.0            RCurl_1.95-4.8           biomaRt_2.30.0          
[22] rtracklayer_1.34.2       multtest_2.30.0          pkgmaker_0.22           
[25] openssl_0.9.6            GEOquery_2.40.0          quadprog_1.5-5          
[28] codetools_0.2-8          matrixStats_0.51.0       XML_3.98-1.5            
[31] reshape_0.8.6            GenomicAlignments_1.10.1 MASS_7.3-29             
[34] bitops_1.0-6             grid_3.3.1               nlme_3.1-113            
[37] xtable_1.8-2             registry_0.3             DBI_0.6                 
[40] magrittr_1.5             stringi_1.1.3            genefilter_1.56.0       
[43] doRNG_1.6                limma_3.30.13            nor1mix_1.2-2           
[46] RColorBrewer_1.1-2       siggenes_1.48.0          tools_3.3.1             
[49] illuminaio_0.16.0        rngtools_1.2.4           survival_2.37-7         
[52] AnnotationDbi_1.36.2     beanplot_1.2             memoise_1.0.0           
> biocValid()
[1] TRUE
> traceback()
20: as.vector(x, mode)
19: as.vector(x, mode = "integer")
18: .local(x, ...)
17: as.integer(seqnames(x))
16: as.integer(seqnames(x))
15: get_out_of_bound_index(x)
14: valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE)
13: valid.func(object)
12: validityMethod(as(object, superClass))
11: anyStrings(validityMethod(as(object, superClass)))
10: validObject(.Object)
9: initialize(value, ...)
8: initialize(value, ...)
7: new(Class, seqnames = seqnames, ranges = ranges, strand = strand,
       elementMetadata = mcols, seqinfo = seqinfo)
6: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges,
       strand = strand, mcols = mcols, seqlengths = seqlengths,
       seqinfo = seqinfo)
5: GRanges(seqnames = locs$chr, ranges = IRanges(start = locs$pos,
       width = 1))
4: getLocations(object, mergeManifest = mergeManifest, orderByLocation = TRUE,
       lociNames = featureNames(object))
3: .local(object, ...)
2: mapToGenome(MsetEx.sub)
1: mapToGenome(MsetEx.sub) at #4