Question

Unknown annotation in the RGChannelSetExtended object

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Frocha ▴ 20

@frocha-12039

Last seen 6.5 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 • 2.3k views

ADD COMMENT • link updated 7.7 years ago by xue.zhang • 0 • written 7.7 years ago by Frocha ▴ 20

score 0 · Answer 1 · 2017-03-15

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xue.zhang • 0

@xuezhang-12601

Last seen 7.7 years ago

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

ADD COMMENT • link 7.7 years ago xue.zhang • 0

score 0 · Answer 2 · 2017-03-15

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xue.zhang • 0

@xuezhang-12601

Last seen 7.7 years ago

hi, run this

rgSet@annotation=c(array="IlluminaHumanMethylationEPIC",annotation="ilm10b2.hg19")

ADD COMMENT • link 7.7 years ago xue.zhang • 0

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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"

ADD REPLY • link 7.7 years ago Martin Morgan 25k