I'm not able to import data with champ.load. I don't know if it's a minfi error?
> myLoad <- champ.load(arraytype = "EPIC")
[===========================]
[<<<< ChAMP.LOAD START >>>>>]
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[ Loading Data with ChAMP Method ]
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Note that ChAMP method will NOT return rgSet or mset, they object defined by minfi. Which means, if you use ChAMP method to load data, you can not use SWAN or FunctionNormliazation method in champ.norm() (you can use BMIQ or PBC still). But All other function should not be influenced.
[===========================]
[<<<< ChAMP.IMPORT START >>>>>]
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[ Section 1: Read PD Files Start ]
CSV Directory: %MyDir%/Sample_setup.csv
Find CSV Success
Reading CSV File
Error in if (skip > 0L) readLines(file, skip) :
argument is of length zero
> traceback()
6: read.table(file = file, header = header, sep = sep, quote = quote,
dec = dec, fill = fill, comment.char = comment.char, ...)
5: read.csv(csvfile, skip = which(substr(readLines(csvfile), 1,
6) == "[Data]"), stringsAsFactor = FALSE, header = TRUE)
4: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
3: suppressWarnings(pd <- read.csv(csvfile, skip = which(substr(readLines(csvfile),
1, 6) == "[Data]"), stringsAsFactor = FALSE, header = TRUE))
2: champ.import(directory, arraytype = arraytype)
1: champ.load(arraytype = "EPIC")
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_2.2.1 ChAMP_2.8.3
[3] IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.12.0
[5] DMRcate_1.12.1 DMRcatedata_1.12.0
[7] DSS_2.16.0 bsseq_1.12.1
[9] FEM_3.4.0 graph_1.54.0
[11] org.Hs.eg.db_3.4.1 impute_1.50.1
[13] igraph_1.0.1 corrplot_0.77
[15] marray_1.54.0 limma_3.32.2
[17] Matrix_1.2-10 AnnotationDbi_1.38.1
[19] ChAMPdata_2.8.1 minfi_1.22.1
[21] bumphunter_1.16.0 locfit_1.5-9.1
[23] iterators_1.0.8 foreach_1.4.3
[25] Biostrings_2.44.1 XVector_0.16.0
[27] SummarizedExperiment_1.6.3 DelayedArray_0.2.7
[29] matrixStats_0.52.2 Biobase_2.36.2
[31] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2
[33] IRanges_2.10.2 S4Vectors_0.14.3
[35] BiocGenerics_0.22.0 BiocInstaller_1.26.0
I just tried with ChAMP v. 2.6.x, no problem loading here.
My CSV-files look something like this, I of course save them with commas as separators:
Hello Rasmus:
I think the reason is champ.import() read .csv file from illumina machine, normally those csv files contain some additional information ahead, like date or producer's name. So champ.import() would filter them ahead, then read data. I think your data have been modified before, because the first line is already information of samples.
It's easy to fix, just open your .csv file, and add one line "[Data]" ahead of it, then champ.import() should be able to recognize it. like:
[Data]
Sample_Name
Real_Name
Sample_Group
Conversion
Sample_Plate
Sample_Well
Array
Slide
Basename
1
s1
CTRL
1
1
F3
R06C01
201247480020
201247480020_R06C01
2
s2
CTRL
1
1
H3
R08C01
201247480020
201247480020_R08C01
Then it should work.
Note that for Chinese users or other special language users, I don't recommend you use Excel to do this, because based on my experience, if you open .csv file with Excel, then close it with saving, the format would be changed. I am not sure if it's related to lauguage or Excel, but it never works for me.
Best
Yuan Tian