The situation described (of a shift in the mean fluorescence intensity of the whole population of cells on aantibody staining) is quite common. In my view, it would be incorrect (indeed, meaningless) to subtract away the isotype control fluorescence and then to describe the remaining cells as 'positive'. The whole population is positive, the observation that the positive and negative populations overlap is irrelevant. In this type of experiment, you are not trying to identify positive and negative sub-sets but looking at the expression of an antigen across the whole population. In these experiments, I always express the results as either the mean or the median fluorescence intensity of the whole population. It could be legitimate to subtract the MFI of the isotype control to express the result as the increase in MFI due to antibody binding. Michael Ormerod 34 Wray Park Road Reigate RH2 ODE Telephone: voice & FAX: (0)1737 241726 Web site: http://ourworld.compuserve.com/homepages/Michael_Ormerod
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