Hello out there flow-folk, I am working with transformed haemopoietic cell lines, treating them with cytokine, and measuring the expression of surface markers by single colour flow. I would appreciate advise on how to analyze the following situation: My problem is that in response to cytokine, a number of the lines increase in size, granularity, as well as showing a significant increase in autofluorescence (e.g. with the same settings FL1, FL2 medians go from approximately 6 and 9 to 11 and 27 respectively). How should I interpret positive markers which show a similar log increase? I believe a sensible thing to do is to use a spare fluorescence channel to compensate for autofluorescence. However is compensation applied to just the treated data set/samples, or is this bad behavior and the same compensation should be applied to both conditions? Thanks in advance, Jason. Jason Gush Malaghan Institute of Medical Research P.O. Box 7060. Wellington, NEW ZEALAND.
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