Error using methylumi.bgcorr for processing of Illumina array data
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
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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.