RnBeads data preprocessing error
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Entering edit mode
Clyndas • 0
@clyndas-14277
Last seen 4.9 years ago

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!!

 

RnBeads • 872 views
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Entering edit mode
mlyall • 0
@mlyall-7242
Last seen 4.5 years ago
United Kingdom

 

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

Many thanks

Marcus

 

 

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