Hi all,

I am very new to all of this.

I’m running into a warning when running wateRmelon::BMIQ on a methylset object (from Illumina EPIC 850k). I have ~1500 samples.

Since I am using a methylset object, I have no arguments to the function other than the object.

The object has been filtered to remove some samples and some probes, and I have run minfi::preprocessNoob on it before BMIQ.

I get the below set of errors twice (so, a total of 8 errors).

In general, I expect that this means something is missing entirely. How do I drill down to understand what is missing? And is this likely a sample-based problem, a probe-based problem, or something else? Also, is this hugely problematic (indicative that I have done something terribly wrong) or is this likely to mean that a few of my (samples?) have issues?

Thank you so much for any guidance making sense of this!

## Warning in min(beta2.v[rand.idx[subsetclass2.v == 2]]): no non-missing
## arguments to min; returning Inf
## Warning in max(beta2.v[rand.idx[subsetclass2.v == 2]]): no non-missing
## arguments to max; returning -Inf
## Warning in max(beta2.v[selU.idx]): no non-missing arguments to max; returning
## -Inf
## Warning in max(nbeta2.v[selU.idx]): no non-missing arguments to max; returning
## -Inf