minfi: delete NA values from RGChannelSet

Question

[philipp24]

Dear all,

it´s probably a simple question, however I can´t find a proper solution yet. I process a 450k methlyation dataset with the minfi package. I noticed that there are 2523 NA values when I extract beta values from the RGChannelSet. The simple question is how I should proceed with these NA values i.e. how can I yield a RGChannelSet without features having NA?

Thanks,

Philipp

>RGSet
RGChannelSet (storageMode: lockedEnvironment)
assayData: 622399 features, 129 samples 
  element names: Green, Red 
An object of class 'AnnotatedDataFrame'
  sampleNames: 1 2 ... 129 (129 total)
  varLabels: ID txt ... param (106 total)
  varMetadata: labelDescription
Annotation
  array: IlluminaHumanMethylation450k
  annotation: ilmn.v1.2

>beta <- getBeta(RGSet)
>sumis.na(beta))  
[1] 2523

[Tanvir Ahamed]

You can impute missing values.