[BioC] methylumi on Infiniium27k idat files

[chris briggs]

I've been using methylumi to extract beta-vals, m-vals, etc. from my 24 idat
files and find many instances of beta values = "NA" even though the detection p
values are far less than 0.05. What causes a beta value of "NA"?

K_samps <-
read.table("KyleA_met27k_Samples_051812.txt",row.names=2,sep='\t',header=T)

K_idat<-methylumIDAT(barcodes = K_samps$barcode, pdat = K_samps)

K_bgcorr <- methylumi.bgcorr(K_idat) 

K_betaVals <-betas(K_bgcorr )