Unknown annotation in the RGChannelSetExtended object
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Frocha ▴ 10
@frocha-12039
Last seen 3.2 years ago

I use read.metharray.exp() in the minfi package to read .IDAT files from Illumina MethylationEPIC array. I got an unknown annotation:

> rgSet<-read.metharray.exp(base="IDAT/",extended=TRUE)
> rgSet
RGChannelSetExtended (storageMode: lockedEnvironment)
assayData: 1051943 features, 8 samples
  element names: Green, GreenSD, NBeads, Red, RedSD
An object of class 'AnnotatedDataFrame': none
Annotation
  array: Unknown
  annotation: Unknown

Why the annotation is unknown? Thanks!
 

minfi idat annotation EPIC • 1.1k views
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xue.zhang • 0
@xuezhang-12601
Last seen 4.4 years ago

having the same problem with EPIC. tried with minfi 450k sample data, no problem.

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Looks like 'RGChannelSetExtendeds' is based on the ExpressionSet class, and so using an accessor rather than direct slot access is much preferred.

> eset = ExpressionSet()
> annotation(eset)
character(0)
> annotation(eset) = c("foo", "bar")
> annotation(eset)
[1] "foo" "bar"

 

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