Error in if (magic != "IDAT") { : argument is of length zero
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rawdata <- loadData(idatPath = "~/epigenetics/data")
Loading idat files.
[read.metharray.sheet] Found the following CSV files:
[1] "/home/qli2/epigenetics/data/targets2_mod.csv"
Error in if (magic != "IDAT") { : argument is of length zero
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Timing stopped at: 112.9 0.681 234.6
Could you please advise what this error message mean? If I started with the RGChannelSet that I created separately, I ran into the following situaton:
dataset_ALL <- normalizeData(RGset=rgSet, normMethod = "ALL") #failed probably due to the QN method
Loading RGset object.
Dataset has 225 samples.
Error in TypeII.Green[rnms_QN_TypeII, ] : subscript out of bounds
class(rgSet)
[1] "RGChannelSet"
attr(,"package")
[1] "minfi"
dataset_QN <- normalizeData(RGset=rgSet, normMethod = "QN") #doesn't work gave the same error above
dataset_SQN <- normalizeData(RGset=rgSet, normMethod = "SQN") #time consuming but works
Thanks for your insight!