I found a small problem with ttestFun in marrayTools which should be addressed. When all the spots are NA the function returns NA. But when there is one good spot, the function bombs. Since you cannot do a t-test with one spot the function should return NA if there are fewer than 2 "good" spots. (Actually, I'd be happier to make this 3, but at least you can do the computation with 2.) Thanks Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111