Hi,

I have the same problem that the one observed in this question DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed, however my data has not NA values both in M-values matrix and after fitting model with limma

This is what I have done:

```
Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In logit2(assay(object, "Beta")) : NaNs produced
2: In logit2(assay(object, "Beta")) : NaNs produced
3: Partial NA coefficients for 72970 probe(s)
This is what I have done:
design2 <- model.matrix(~0+location + sex + age)
cm2 <- makeContrasts(
ProximalvsDistal = proximal - distal,
ProximalvsRectum = proximal - rectum,
DistalvsRectum = distal - rectum,
levels=design2)
fit2 <- lmFit(MVals, design2)
fit2 <- contrasts.fit(fit2, cm2)
efit2 <- eBayes(fit2, robust = TRUE)
naind <- is.na(rowSums(efit2$p.value))
naind[which(naind=='TRUE')]
#named logical(0)
```

Also I have checked that my M-values matrix has no NAs

```
apply(is.na(MVals), 2, which)
#integer(0)
```

Any suggestions would be much appreciated