Question: error in density plot - methylation EPIC data
gravatar for junehicks0
6 months ago by
junehicks010 wrote:

I am creating densityplot for methylation EPIC data using minfi package in R

Below is my code for plotting density plot

rgsetAll <- read.metharray.exp(targets = Targets, force=TRUE)
densityPlot(preprocessRaw(rgsetAll), main = "Methylation")

However i'm getting this error:

Error in density.default(newX[, i], ...) : 
  need at least 2 points to select a bandwidth automatically
Calls: densityPlot -> apply -> FUN -> FUN -> density.default

I checked beta values and there is a lot of missing values (NA) for couple of samples. Could missing values be causing error?

Did anyone face this problem while dealing with methylation array data.

Any help is appreciated

bioconductor R • 242 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 6 months ago by junehicks010
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