Dear Sir/Mrs.

If I would like to compare surface expression of a specific antigen in two similar (but not identical) cell lines, how should I do it? (I want to have numbers I could write)

One cell line is derived from the other (by transfection) and I would like to know whether other, irrelevant, surface proteins, are also changed. The Iotype controls are similar but not identical for the 2 cell lines, so should I devide/substract the isotype control Median Fluoresence of each sample from the meidian fluoresence of the positively-stained sample? I cannot detrmine precent of positively-labeled cells since I see a shift in the whole population.

Hope the question is clear...
Thanks, Tamat Oved Gelber