Problem loading Red channel idat files with champ.load
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Paulina • 0
@9040956b
Last seen 7 weeks ago
United States

Hello, I am relatively new to methylation data analysis but have successfully run a small analysis using ChAMP. I am now trying to do so on a larger data set and am having difficulty loading the idat files. This is my code and the error message. As you can see it loads the Green (Grn) files without issues and then has an error when loading the Red files. I have checked and the Red files are complete and present in the same directory as the Green files. Of note, I abbreviated the result section for length. Thank you for your help.

myLoad <- champ.load(directory = dataDirectory, arraytype = "EPIC", force = TRUE)
[===========================]
[<<<< ChAMP.LOAD START >>>>>]
-----------------------------
[ Loading Data with ChAMP Method ]
----------------------------------

[===========================]
[<<<< ChAMP.IMPORT START >>>>>]
-----------------------------
[ Section 1: Read PD Files Start ]
  CSV Directory: /Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/Sample_sheet.csv
  Find CSV Success
  Reading CSV File
  Replace Sentrix_Position into Array
  Replace Sentrix_ID into Slide
[ Section 1: Read PD file Done ]
[ Section 2: Read IDAT files Start ]
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/204776850055/204776850055_R01C01_Grn.idat ---- (1/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/203287590047/203287590047_R01C01_Grn.idat ---- (2/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/204076520162/204076520162_R05C01_Grn.idat ---- (3/301)
...
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/203287590038/203287590038_R01C01_Grn.idat ---- (300/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/203287590090/203287590090_R01C01_Grn.idat ---- (301/301)

  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/204776850055/204776850055_R01C01_Red.idat ---- (1/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/203287590047/203287590047_R01C01_Red.idat ---- (2/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/204076520162/204076520162_R05C01_Red.idat ---- (3/301)
...
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/204076520014/204076520014_R03C01_Red.idat ---- (70/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/204813570046/204813570046_R03C01_Red.idat ---- (71/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/204813570046/204813570046_R07C01_Red.idat ---- (72/301)
  Loading:/Users/pgl/Desktop/Northwestern/Research/Methylation/PPMI_docs/METH/Meth_Oct21/203867050053/203867050053_R07C01_Red.idat ---- (73/301)

Error in while (m%/%128 == 1) { : argument is of length zero

> traceback()
10: readString(con = con)
9: readField(con = con, field = xx)
8: FUN(X[[i]], ...)
7: lapply(res, function(xx) {
       where <- fields[xx, "byteOffset"]
       seek(con, where = where, origin = "start")
       readField(con = con, field = xx)
   })
6: readIDAT_nonenc(file, what = what)
5: readIDAT(x)
4: FUN(X[[i]], ...)
3: lapply(RedPath, function(x) {
       message("  Loading:", x, " ---- (", which(RedPath == x), 
           "/", length(RedPath), ")")
       readIDAT(x)
   })
2: champ.import(directory, arraytype = arraytype)
1: champ.load(directory = dataDirectory, arraytype = "EPIC", force = TRUE)

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib  
sessionInfo( )
R MethylationArrayData ChAMP • 71 views
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