I would like to take this opportunity to introduce myself. I am currently working on analyzing Illumina 450k Methylation Array dataset using 
minfi Package.
I got the following error message while I call the dmpFinder function: 

dmp <- dmpFinder(mset, pheno=pd$Sample_Group, type="categorical")
Error in smooth.spline(lambda, vec.p0, w = ncs.weights, df = 3) : 
  missing or infinite values in inputs are not allowed
In addition: Warning messages:
1: Partial NA coefficients for 44 probe(s) 
2: In pf(q, df1, df2, lower.tail, log.p) : NaNs produced

I have traced out the error message and found that some missing values in my dataset: 
> sum(is.na(getM(RGset)))
[1] 28

Could you please advise how can I removed these missing values
 records from the dataset (i.e., RGset <- read.450k.exp (base = baseDir, targets = targets))?

Regards,

Haroon 

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