Is flagging the same as filtering?  In my Limma script it takes only those ESTs with a flag of 0 (which are good spots). 

myfun <- function(x) as.numeric ( x$Flag >0)  

 Is this not the same as filtering?  If I actually remove the absent spots from my Imagene files, then the files each have different lengths and the order of genes is not the same in each file.

Sally
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