Hi,
I am analyzing the affy microarray data with >10 conditions in triplicates. I would like to know, what is the cut-off or the best way to use MAS5 present/absent calls.
Can I just remove probes that are absent in all conditions?
In R, I do:
calls <- mas5calls(eset1);
calls <- exprs(calls);
absent <- rowSums(calls == 'A');
Or is there any other more commonly used cut-off for the present/absent calls?
Thanks in advance.
Diwan