(I recently posted an empty message with almost the same subject. I tried to resend it, but unfortunately our email servers were down. Here is an updated version). I am looking at expanding the image methid for an AffyBatch object, in the sense that I only want to plot certain (x,y) coordinates. I ahve therefore looked at the code and have a little problem understanding why it is done as it is. This problem might be because I am unsure where the (0,0) position on the chips is. For some reason I have assumed it would be the upper, left corner - but I have no evidence for that Bascially the code I have a problem with is m <- x@exprs[, i] ### Some deleted stuff m <- as.matrix(rev(as.data.frame(matrix(m, nrow = length(x.pos), ncol = length(y.pos))))) "m" is then used as the "z" argument of image. If I do > m <- matrix(1:9, ncol = 3) > m [,1] [,2] [,3] [1,] 1 4 7 [2,] 2 5 8 [3,] 3 6 9 Here the number in the matrix takes the lace of indices, which have the following (x,y) coordinates > indices2xy(1:9, nr = 3) x y [1,] 0 0 [2,] 1 0 [3,] 2 0 [4,] 0 1 [5,] 1 1 [6,] 2 1 [7,] 0 2 [8,] 1 2 [9,] 2 2 If I do > m1 <- as.matrix(rev(as.data.frame(m))) > m1 V3 V2 V1 1 7 4 1 2 8 5 2 3 9 6 3 > image(1:3, 1:3, m1) I seem to get a plot where the (0,0) position is at the lower, right corner, and increasing (x,y) means going to the left and up. Basically, m1 = m[, 3:1] If I instead do > image(1:3, 1:3, m[3:1,]) I seem to get the right plot. It seems to me that the image method rotates the chip 90 degress, but in the wrong direction. Am I completely off, or? Kasper