The following code should do it. This assumes matrices a and x are of the same dimension which is why you can index a as below x[is.na(x)==TRUE]<-a[is.na(x)==TRUE] -- View this message in context: http://www.nabble.com/Combine-two-matricies-tp24458609p24458797.html Sent from the R help mailing list archive at Nabble.com.