I am measuring IL-2, interferon gamma, IL-17 and a number of other genes in memory CD4 T cells after polyclonal activation with anti-CD3. I am using expression of GAPDH as a housekeeping (after efficiency determination) to calculate deltaCt. However, since there is no basal cytokine expression, I don't use basal expression to normalize; i.e., calculate a deltaDeltaCt, since this would require assigning a value of zero to basal conditions.
How are results like this presented graphically?
What is the best read out, plain deltaCts?