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Question: RnBeads data preprocessing error
0
gravatar for Clyndas
11 months 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 6 months ago by mlyall0 • written 11 months ago by Clyndas0
0
gravatar for mlyall
6 months ago by
mlyall0
United Kingdom
mlyall0 wrote:

 

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

Many thanks

Marcus

 

 

ADD COMMENTlink written 6 months ago by mlyall0
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