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Analysis of high throughput screen for cell surface markers - (Jan/31/2012 )


I'm totally new to the world of flow cytometry data analysis and am looking for some help. I have 4 cell lines that were analyzed by high throughput screen flow cytometry for over 300 CD and other surface molecules. I received an excel file with MFI and %gate+ for each molecule for each cell line. I want to compared the level of expression between the cell lines. My questions are:

1) How do I normalized the data (I do not have a control or anything)
2) Do I use MFI or %gate+ for the anaylsis. For either, what is a good cut-off value (i.e. what is background level?)
3) How do I normalize the data?

Any insight would be greatly appreciated!


Do all of your cells express the proteins of interest. There might be some negative cell lines and maybe you could use them for comparison.