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!!
