missMethyl and Error About Missing Value

Question

[Indira]

My goal: To use missMethyl to process the data I have.

My problem: When I follow along with the missMethyl manual I come across an error that does not seem to make sense to me:

Attempt 1:

rfit1 <- RUVfit(Y = Mc, X = grp, ctl = ctl1) # Stage 1 analysis
rfit2 <- RUVadj(Y = Mc, fit = rfit1)

My error:

Error in if (temp[[4]] > 0) df = df + temp[[4]] else df = Inf: missing value where TRUE/FALSE needed Traceback:

1. RUVadj(Y = Mc, fit = rfit1)
2. ruv::ruv_summary(Y, fit, colinfo = cpginfo, var.type = var.type, . p.type = p.type, ...)
3. variance_adjust(fit)
4. sigmashrink(fit$sigma2, fit$df)

I am unsure as to why this error is occurring and I don't know what I can change in order to not get this error. I have tried modifying the code before however, it seems like I am doing something incorrectly. Does anyone know what that in and how I could possibly correct it?

[Sam]

Can you share what platform you are running on? I am having a similar problem on arm64 MacOS (M1): I noticed the few other mentions of this issue online started popping up around 2020/2021 so I'm thinking it might be architecture related.