Different MOI in comparison experiment - (Jan/31/2014 )

I infected two cells with IAV using two different MOI, one of them 1 and the other is 10. Now I wanted to compare the expression level of one miRNA in both  cells. I think this is not right to compare. Since I did the experiment, has anyone any suggestion to surmount or overcome this mistake without repeating the experiment.   any suggestion

Why is it not right - as far as I can see, all you are comparing is the difference between two different infection amounts, so there shouldn't be a problem.  The results can be normalized to a cellular gene that isn't affected by the infection.

But the problem I think is that when u hit the cells with a high MOI, more cells died while still  a live in the other low MOI and this affect the expression of cell genes. Which to normalize to  a gene that not affected by infection ? like B actin For example ?

Yes, dying cellare a problem, however DNA and RNA are rapidly degraded during apoptosis.

As to the gene - check the literature.  many viruses alter actin expression.