PCA on transposed data

I had the same problem. For me, it worked when I assigned column names (other than numeric) to my data.frame. For example, when colnames(mydf) was (1,2,3,4,5), I got this error:

Error in [.data.frame(mf, , x) : undefined columns selected

What I did was:

colnames(mydf) <- paste("var", 1:5, sep="")

and then ran the princomp function:

mypca <- princomp(~. , data=myrdf, cor=F, na.action=na.exclude)

and had no problems.

Seems like R does not like it when there is missing data and you try to use a formula with all of the variables. So this ended up working:

pca2<-prcomp(na.omit(data_t), scale=TRUE)

of course this omits those columns with missing data.