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Question: RnBeads data preprocessing error
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gravatar for Clyndas
21 days ago by
Clyndas0
Clyndas0 wrote:

Hi,

I am using RnBeads to analyze 450K array data. In the data preprocessing step (after data import), but keep getting this error:

Error in if (any(methylated(x) <= 0)) { :
  missing value where TRUE/FALSE needed

traceback got the following:

> traceback()
10: methylumi.bgcorr(object, method = bgcorr.methylumi)
9: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
8: suppressMessages({
       sinkfile <- ifelse("Windows" %in% Sys.info(), "NUL", "/dev/null")
       sink(sinkfile)
       object <- methylumi.bgcorr(object, method = bgcorr.methylumi)
       sink()
   })
7: rnb.execute.normalization(object, method)
6: rnb.step.normalization(rnb.set, report)
5: rnb.run.preprocessing(rnb.set.unfiltered, dir.reports = report.dir) at run_rnb_qqplot_2.R#45
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("run_rnb_qqplot_2.R")

Here is the relevant code:

result <- rnb.run.import(data.source=data.source, data.type="infinium.idat.dir", dir.reports=report.dir)
rnb.set <- result$rnb.set
rnb.set.unfiltered <- rnb.set
result <- rnb.run.preprocessing(rnb.set.unfiltered, dir.reports=report.dir) 

I tried to seperate the filtering step with normalization step, but got the same error even using the unfiltered data.

Can anyone give some ideas of how to fix it?

Thanks for your help in advance!!

 

ADD COMMENTlink modified 21 days ago • written 21 days ago by Clyndas0
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