Question: Unknown annotation in the RGChannelSetExtended object
0
gravatar for Frocha
2.6 years ago by
Frocha10
Frocha10 wrote:

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!
 

annotation minfi idat epic • 839 views
ADD COMMENTlink modified 2.5 years ago by xue.zhang0 • written 2.6 years ago by Frocha10
Answer: Unknown annotation in the RGChannelSetExtended object
0
gravatar for xue.zhang
2.5 years ago by
xue.zhang0
xue.zhang0 wrote:

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

ADD COMMENTlink written 2.5 years ago by xue.zhang0
Answer: Unknown annotation in the RGChannelSetExtended object
0
gravatar for xue.zhang
2.5 years ago by
xue.zhang0
xue.zhang0 wrote:

hi, run this

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

ADD COMMENTlink written 2.5 years ago by xue.zhang0

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 REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 295 users visited in the last hour