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Question: Illumina EPIC array annotation error
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gravatar for gammyknee
3 months ago by
gammyknee10
Australia/Adelaide
gammyknee10 wrote:

Hi Everyone,

Im currently trying to analyse a large number of EPIC arrays and I'm getting an odd package error that seems to come about when I add annotation to the array object

rgSet <- read.metharray.exp(targets = targets)

getManifest(rgSet)

annotation(rgSet)[1] <- "IlluminaHumanMethylationEPIC" annotation(rgSet)[2] <- "ilm10b2.hg19"

mSet <- preprocessSWAN(rgSet)

detP <- detectionP(rgSet) keep <- rowSums(detP < 0.05) == ncol(rgSet) mSet <- mSet[keep,]

dim(mSet)

RSet <- ratioConvert(mSet, what = "both", keepCN = TRUE) GRset <- mapToGenome(RSet)

It completes fine, but when looking at RSet or GRset I get:

RSet <- ratioConvert(mSet, what = "both", keepCN = TRUE)
> RSet
class: RatioSet 
dim: 848005 192 
metadata(0):
assays(3): Beta M CN
rownames(848005): cg18478105 cg09835024 ... cg10633746 cg12623625
rowData names(0):
colnames(192): 201236470086_R01C01 201236470086_R02C01 ... 201364910019_R05C01
      201364910105_R05C01
colData names(9): Sample_Name Sample_Well ... Basename filenames
Annotation
Error in seq.default(along = annotation) : 
      (converted from warning) partial argument match of 'along' to 'along.with'    

I know this is just probably a package conflict and that it does look like seq.default has changed an argument from along to along.with, but considering the basic nature of this function in an array analysis pipeline, I was wondering whether anyone had seen this before?

Cheers

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8       
 [4] LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] pander_0.6.0                                       
 [2] stringr_1.2.0                                      
 [3] Rgraphviz_2.20.0                                   
 [4] GMCM_1.2.4                                         
 [5] GOstats_2.42.0                                     
 [6] graph_1.54.0                                       
 [7] Category_2.42.1                                    
 [8] Matrix_1.2-10                                      
 [9] GO.db_3.4.1                                        
[10] biomaRt_2.32.1                                     
[11] RColorBrewer_1.1-2                                 
[12] gridExtra_2.2.1                                    
[13] qqman_0.1.4                                        
[14] pheatmap_1.0.8                                     
[15] methylumi_2.22.0                                   
[16] FDb.InfiniumMethylation.hg19_2.2.0                 
[17] org.Hs.eg.db_3.4.1                                 
[18] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2            
[19] GenomicFeatures_1.28.4                             
[20] AnnotationDbi_1.38.2                               
[21] reshape2_1.4.2                                     
[22] scales_0.4.1                                       
[23] limma_3.32.5                                       
[24] ggbio_1.24.1                                       
[25] ggrepel_0.6.5                                      
[26] magrittr_1.5                                       
[27] plyr_1.8.4                                         
[28] readxl_1.0.0                                       
[29] dplyr_0.7.2                                        
[30] purrr_0.2.3                                        
[31] readr_1.1.1                                        
[32] tidyr_0.6.3                                        
[33] tibble_1.3.3                                       
[34] ggplot2_2.2.1                                      
[35] tidyverse_1.1.1                                    
[36] missMethyl_1.10.0                                  
[37] IlluminaHumanMethylationEPICmanifest_0.3.0         
[38] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[39] BiocInstaller_1.26.0                               
[40] minfi_1.22.1                                       
[41] bumphunter_1.16.0                                  
[42] locfit_1.5-9.1                                     
[43] iterators_1.0.8                                    
[44] foreach_1.4.3                                      
[45] Biostrings_2.44.2                                  
[46] XVector_0.16.0                                     
[47] SummarizedExperiment_1.6.3                         
[48] DelayedArray_0.2.7                                 
[49] matrixStats_0.52.2                                 
[50] Biobase_2.36.2                                     
[51] GenomicRanges_1.28.4                               
[52] GenomeInfoDb_1.12.2                                
[53] IRanges_2.10.2                                     
[54] S4Vectors_0.14.3                                   
[55] BiocGenerics_0.22.0                                

loaded via a namespace (and not attached):
  [1] RSQLite_2.0                                       
  [2] htmlwidgets_0.9                                   
  [3] BiocParallel_1.10.1                               
  [4] munsell_0.4.3                                     
  [5] codetools_0.2-15                                  
  [6] preprocessCore_1.38.1                             
  [7] statmod_1.4.30                                    
  [8] colorspace_1.3-2                                  
  [9] OrganismDbi_1.18.0                                
 [10] knitr_1.16                                        
 [11] GenomeInfoDbData_0.99.0                           
 [12] mnormt_1.5-5                                      
 [13] bit64_0.9-7                                       
 [14] biovizBase_1.24.0                                 
 [15] R6_2.2.2                                          
 [16] illuminaio_0.18.0                                 
 [17] AnnotationFilter_1.0.0                            
 [18] bitops_1.0-6                                      
 [19] reshape_0.8.6                                     
 [20] assertthat_0.2.0                                  
 [21] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
 [22] nnet_7.3-12                                       
 [23] gtable_0.2.0                                      
 [24] ensembldb_2.0.3                                   
 [25] rlang_0.1.1                                       
 [26] genefilter_1.58.1                                 
 [27] calibrate_1.7.2                                   
 [28] splines_3.4.0                                     
 [29] rtracklayer_1.36.4                                
 [30] lazyeval_0.2.0                                    
 [31] acepack_1.4.1                                     
 [32] GEOquery_2.42.0                                   
 [33] dichromat_2.0-0                                   
 [34] broom_0.4.2                                       
 [35] checkmate_1.8.3                                   
 [36] yaml_2.1.14                                       
 [37] modelr_0.1.1                                      
 [38] backports_1.1.0                                   
 [39] httpuv_1.3.5                                      
 [40] Hmisc_4.0-3                                       
 [41] RBGL_1.52.0                                       
 [42] tools_3.4.0                                       
 [43] psych_1.7.5                                       
 [44] nor1mix_1.2-2                                     
 [45] siggenes_1.50.0                                   
 [46] Rcpp_0.12.12                                      
 [47] base64enc_0.1-3                                   
 [48] zlibbioc_1.22.0                                   
 [49] RCurl_1.95-4.8                                    
 [50] BiasedUrn_1.07                                    
 [51] rpart_4.1-11                                      
 [52] openssl_0.9.6                                     
 [53] haven_1.1.0                                       
 [54] cluster_2.0.6                                     
 [55] data.table_1.10.4                                 
 [56] ProtGenerics_1.8.0                                
 [57] hms_0.3                                           
 [58] mime_0.5                                          
 [59] xtable_1.8-2                                      
 [60] XML_3.98-1.9                                      
 [61] mclust_5.3                                        
 [62] compiler_3.4.0                                    
 [63] htmltools_0.3.6                                   
 [64] Formula_1.2-2                                     
 [65] lubridate_1.6.0                                   
 [66] DBI_0.7                                           
 [67] MASS_7.3-47                                       
 [68] quadprog_1.5-5                                    
 [69] bindr_0.1                                         
 [70] forcats_0.2.0                                     
 [71] pkgconfig_2.0.1                                   
 [72] GenomicAlignments_1.12.1                          
 [73] registry_0.3                                      
 [74] IlluminaHumanMethylation450kmanifest_0.4.0        
 [75] foreign_0.8-69                                    
 [76] xml2_1.1.1                                        
 [77] annotate_1.54.0                                   
 [78] rngtools_1.2.4                                    
 [79] pkgmaker_0.22                                     
 [80] multtest_2.32.0                                   
 [81] beanplot_1.2                                      
 [82] ruv_0.9.6                                         
 [83] AnnotationForge_1.18.1                            
 [84] rvest_0.3.2                                       
 [85] doRNG_1.6.6                                       
 [86] VariantAnnotation_1.22.3                          
 [87] digest_0.6.12                                     
 [88] base64_2.0                                        
 [89] cellranger_1.1.0                                  
 [90] htmlTable_1.9                                     
 [91] GSEABase_1.38.0                                   
 [92] curl_2.8.1                                        
 [93] shiny_1.0.3                                       
 [94] Rsamtools_1.28.0                                  
 [95] nlme_3.1-131                                      
 [96] jsonlite_1.5                                      
 [97] bindrcpp_0.2                                      
 [98] BSgenome_1.44.0                                   
 [99] lattice_0.20-35                                   
[100] GGally_1.3.2                                      
 [ reached getOption("max.print") -- omitted 10 entries ]

>
ADD COMMENTlink modified 3 months ago by James W. MacDonald45k • written 3 months ago by gammyknee10
1
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald45k wrote:

Why are you bothering to put the annotation information into your RGChannelSet? It is generated automatically, but then you are hijacking the process and adding incorrect information! In other words, you don't have to add the annotation to the object - it's added automatically. And if you over-write the correctly instantiated annotation vector with the wrong thing you are likely to get problems.

Do note that the annotation slot of an RGChannelSet is a named vector of length 2, and you are replacing the (correctly formed) vector with an un-named vector, which is causing problems.

ADD COMMENTlink written 3 months ago by James W. MacDonald45k

In addition, it appears your code won't even work as written:

> rawdat
class: RGChannelSet
dim: 1051943 32
metadata(0):
assays(2): Green Red
rownames(1051943): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(32): 201172580002_R01C01 201172580002_R02C01 ...
  201172580056_R07C01 201172580056_R08C01
colData names(9): Sample_Name Sample_Well ... Basename filenames
Annotation
  array: IlluminaHumanMethylationEPIC
  annotation: ilm10b2.hg19
> notok <- rawdat
> annotation(notok) <- c("IlluminaHumanMethylationEPIC","ilm10b2.hg19")
> notok
class: RGChannelSet
dim: 1051943 32
metadata(0):
assays(2): Green Red
rownames(1051943): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(32): 201172580002_R01C01 201172580002_R02C01 ...
  201172580056_R07C01 201172580056_R08C01
colData names(9): Sample_Name Sample_Well ... Basename filenames
Annotation

> notok <- preprocessSWAN(notok)
Error in .getManifestString(object@annotation) :
  unable to get the manifest string for this object
> getManifest(notok)
Error in .getManifestString(object@annotation) :
  unable to get the manifest string for this object
ADD REPLYlink written 3 months ago by James W. MacDonald45k

I was following the advice of someone on the support site which called to manually add EPIC annotations to overwrite the 450K annotation.

Agreed. Even without doing that I'm getting an error:

> rgSet <- read.metharray.exp(targets = targets)
> getManifest(rgSet)
IlluminaMethylationManifest object
Annotation
  array: IlluminaHumanMethylationEPIC
Number of type I probes: 142262 
Number of type II probes: 724574 
Number of control probes: 635 
Number of SNP type I probes: 21 
Number of SNP type II probes: 38 

> rgSet
class: RGChannelSet 
dim: 1051943 192 
metadata(0):
assays(2): Green Red
rownames(1051943): 1600101 1600111 ... 99810990 99810992
rowData names(0):
colnames(192): 201236470086_R01C01 201236470086_R02C01 ... 201364910019_R05C01
  201364910105_R05C01
colData names(9): Sample_Name Sample_Well ... Basename filenames
Annotation
Error in seq.default(along = annotation) : 
  (converted from warning) partial argument match of 'along' to 'along.with'
ADD REPLYlink written 3 months ago by gammyknee10
1

This line:

Error in seq.default(along = annotation) : 
  (converted from warning) partial argument match of 'along' to 'along.with'

Says, in essence, that you would have got a warning because seq.default used partial matching to match the argument 'along' to its actual argument of 'along.which'. But this was converted from a warning to an error because you have the 'warn' option set to 2 or larger, and are converting simple warnings into errors. From ?options

'warn': sets the handling of warning messages.  If 'warn' is
          negative all warnings are ignored.  If 'warn' is zero (the
          default) warnings are stored until the top-level function
          returns.  If 10 or fewer warnings were signalled they will be
          printed otherwise a message saying how many were signalled.
          An object called 'last.warning' is created and can be printed
          through the function 'warnings'.  If 'warn' is one, warnings
          are printed as they occur.  If 'warn' is two or larger all
          warnings are turned into errors.

There are very few reasons to have warnings converted to errors, and I would not recommend that setting for general use.

ADD REPLYlink written 3 months ago by James W. MacDonald45k

Great. Thanks for that explanation 

ADD REPLYlink written 3 months ago by gammyknee10
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