Hello Archana, You didn't mention what kind of chips you used. I would assume they are 22k chips according to your layout design. There is one thing you may need to check. Does your layout file match with your intensity files? I know the agilent scanner output intensity files don't contain those ignore spots. Therefore, the row number of your layout file may be bigger than your intensity files'. Hope it will help! Yanqin --------------------------------- Have fun online with music videos, cool games, IM & more. Check it out! [[alternative HTML version deleted]]