Help with ENmix readidat
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Daphna • 0
@d496d0b3
Last seen 2.1 years ago
United Kingdom

Hi,

I am a complete novice. I'm trying to read idat files using readidat and get the next error

> system("wget http://webdata.illumina.com.s3-website-us-east-1.amazonaws.com/downloads
+ /productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip")
[1] 127
> system("unzip infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip")
[1] 127
> mf="infinium-methylationepic-v-1-0-b5-manifest-file.csv"
> path <- file.path(find.package("minfiData"),"extdata")
> rgSet <- readidat(path = path,manifestfile=mf,recursive = TRUE)

I get this error:

Error in readmanifest(manifestfile) : 
  length(control.line) == 1 && is.integer(control.line) && !is.na(control.line) is not TRUE

sessionInfo( )

R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

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

other attached packages:
 [1] IlluminaHumanMethylationEPICmanifest_0.3.0         minfiData_0.42.0                                  
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 IlluminaHumanMethylation450kmanifest_0.4.0        
 [5] minfi_1.42.0                                       bumphunter_1.38.0                                 
 [7] locfit_1.5-9.5                                     Biostrings_2.64.0                                 
 [9] XVector_0.36.0                                     ENmix_1.32.0                                      
[11] SummarizedExperiment_1.26.1                        Biobase_2.56.0                                    
[13] GenomicRanges_1.48.0                               GenomeInfoDb_1.32.1                               
[15] IRanges_2.30.0                                     S4Vectors_0.34.0                                  
[17] BiocGenerics_0.42.0                                MatrixGenerics_1.8.0                              
[19] matrixStats_0.62.0                                 doParallel_1.0.17                                 
[21] iterators_1.0.14                                   foreach_1.5.2
ENmix IlluminaHumanMethylationEPICmanifest • 833 views
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Did you figure this out? I have the same issue.

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Please don't add to posts from two years ago. Instead make a new post.

Also, please read the help page for readidat. The only reason to specify a manifest file directly is if there isn't already a Bioconductor package (and there is one for the EPIC array, so you can use that one).

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