R function prcomp fails with NA's values even though NA's are allowed

Question

I am using the function prcomp to calculate the first two principal components. However, my data has some NA values and therefore the function throws an error.

Answer 1

Yeah, it looks like a "feature" (bug) that na.action is completely ignored unless you use the formula interface. This has been brought up before on the R Development list.

I think that this should be documented or flagged as a bug.

Just to be clear, this would work because it accesses the formula interface:

prcomp(~V1+V2, data=d, center = TRUE, scale = TRUE, na.action = na.omit)

Answer 2

Another solution if you're not willing to use formula interface is

prcomp(na.omit(d), center = TRUE, scale = TRUE)

which consist of applying na.omit directly to the data frame.