Question: RnBeads data preprocessing error
gravatar for Clyndas
4 months ago by
Clyndas0 wrote:


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%, "NUL", "/dev/null")
       object <- methylumi.bgcorr(object, method = bgcorr.methylumi)
7: rnb.execute.normalization(object, method)
6: rnb.step.normalization(rnb.set, report)
5:, 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 <-, data.type="infinium.idat.dir", dir.reports=report.dir)
rnb.set <- result$rnb.set
rnb.set.unfiltered <- rnb.set
result <-, 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 4 hours ago by mlyall0 • written 4 months ago by Clyndas0
gravatar for mlyall
4 hours ago by
United Kingdom
mlyall0 wrote:


Did you ever solve this issue - I’m having an identical problem!! Any help much appreciated 

Many thanks




ADD COMMENTlink written 4 hours ago by mlyall0
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