Minfi Package - Illumina 450K Methylation Array - Editing Idat Files

Question

[haroon.naeem]

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 some missing values in my dataset:

sumis.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))?

[biohack92]

How did you resolve the error?