Question: minfi: delete NA values from RGChannelSet
0
gravatar for philipp24
22 months ago by
philipp240
philipp240 wrote:

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
minfi R • 674 views
ADD COMMENTlink modified 22 months ago by PoGibas4.7k • written 22 months ago by philipp240

You can impute missing values.

ADD REPLYlink written 21 months ago by Tanvir Ahamed 240
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 2.3.0
Traffic: 525 users visited in the last hour