Error using methylumi.bgcorr for processing of Illumina array data

Question

[Franziska]

When analyzing my EPIC array DNA methylation data I run into troubles when trying to perform the background correction.

My code for the bg correction:

 methylumi.bgcorr(mlimi_set)

And the error I get:

 Error in if (s == 0) stop("cannot estimate scale: MAD is zero for this sample") :  missing value where TRUE/FALSE needed

I couldn't find anything on the manual or Github. Would be really happy if somebody could help me.

Best, Franzi

[jared.andrews07]

Sounds like a data issue, it seems to think there is no variation across the sample. I'm unfamiliar with this package, but you can try to take a look at the values to ensure they aren't all the same value across probes or missing.