Hi All,

I have a basic question. Is it required to filter the microarray data based
on the detection calls (A/M/P) before analyzing it with LIMMA?

What if I have the following scenario (for example):

                           Control Control Control         Treatment
Treatment Treatment
1367813_at           A            A             P
P                   P                 P

Please note that this gene is just "present/detected"  once in the Control,
but it is present in all the replicates of the treatment. In this case: what
would be the right thing to do? To eliminate it from the analysis or keep it
and consider it up or down depending on the signal of the treatment?

Thank a lot!
Avhena

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