Hi, Dear BioC, Is the following a small bug in pamr.knnimpute? pamr.knnimpute<- function (data, k = 10) { x <- data$x N <- dim(x) p <- N[2] N <- N[1] col.nas <- apply(x, 2, is.na) if ((sum(col.nas) == N) > 0) { stop("Error: A column has all missing values!") } Using this, pamr.knnimpute will stop if the total number of missing values in x = nrow(x). > a [,1] [,2] [,3] [,4] [,5] [1,] 1 11 NA 31 41 [2,] 2 12 22 32 NA [3,] NA 13 23 NA 43 [4,] 4 14 NA 34 44 [5,] 5 NA NA 35 45 [6,] NA 16 26 36 46 [7,] 7 17 27 37 47 [8,] 8 18 28 38 48 [9,] 9 19 29 39 49 [10,] NA 20 NA 40 50 > col.nas <- apply(a, 2, is.na) > col.nas [,1] [,2] [,3] [,4] [,5] [1,] FALSE FALSE TRUE FALSE FALSE [2,] FALSE FALSE FALSE FALSE TRUE [3,] TRUE FALSE FALSE TRUE FALSE [4,] FALSE FALSE TRUE FALSE FALSE [5,] FALSE TRUE TRUE FALSE FALSE [6,] TRUE FALSE FALSE FALSE FALSE [7,] FALSE FALSE FALSE FALSE FALSE [8,] FALSE FALSE FALSE FALSE FALSE [9,] FALSE FALSE FALSE FALSE FALSE [10,] TRUE FALSE TRUE FALSE FALSE > sum(col.nas) [1] 10 > N<-dim(a)[1] > N [1] 10 > if ((sum(col.nas) == N) > 0) { + stop("Error: A column has all missing values!") + } Error: Error: A column has all missing values! I've edited it to the use the following rather ugly R code. It does checks if a column contains only NA. knnimpute<- function (data, k = 10) { x <- data$x p <- ncol(x) # P is the ncol of x N <- nrow(x) # N is the nrow of x col.nas <- apply(apply(x, 2, is.na), 2, sum) if (sum(is.element(col.nas,nrow(x)))>0) stop("A column has all missing values!") if (sum(col.nas)/prod(dim(x))>0.15) stop("Greater than 15% missing values in data") # Extra check Regards Aedin