Entering edit mode
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
Did you figure this out? I have the same issue.
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).