GFP vs RFP compensation

Dear flow cytometrists,
 
I would like to get some advice on how to set the compensation between GFP and RFP properly. 
 
I collected my data on a FACSCalibur using CellQuest Pro without compensation and am now trying to use software compensation to get the numbers of GFP+ vs RFP+ and also double positives. So here are my questions:
 
1. Unlike CDsomething antibody staining my GFP is endogenous to the cells and the RFP is added by transfection. There is no clearly defined positive population for either of them, but rather a wide spread - some cells are even squashed against the 10,000 max because they are so bright. So where exactly do I set the regions which are to be used for the software compensation? 
I've tried different regions, but depending on the location, the compensation came out weird. I think I've got something usable now, but could someone more experienced have a look please? I've attached a file showing the gates I used for determining percentages for the relevant controls and the compensation settings FlowJo came up with (unfortunately I seem to have deleted the regions I used for the compensation).
 
I wanted to attach the raw FCS files for the control populations, but seeing as each one is 1Mb I better not. If anyone would be willing to have a look at the data, please email me and I can send the files directly.
 
2. Is there any way I can get plots showing FI of higher than 10,000? Also, when I try to use bi-variate plots in FlowJo, I get very nice resolution around 0 but I'm loosing the >1000 population. I've tried experimenting with the transform values but can't figure out how to make sure the plot still shows the 1,000 - 10,000 events.
 
3. I've tried using FL2 or FL3 for RFP, but I had a lot of unspecific signal in FL3 - kinda looks like PI staining even though I didn't stain my cells with it. I've heard that this can possibly come from PI contaminations in the tubing of FACS machines - is that true? Can I get rid of this problem somehow?
 
Thank you very much for your help
 
Kind regards
 
Petra Disterer
The UCL Inst. of Hepatology
Hampstead Campus U3rd floor
Rowland Hill Street
London
NW3 2PF
UK
This attachment - 'GFP_vs_RFP.jpg' -  125.74 KBytes - can be viewed at
http://www.cyto.purdue.edu/MD-parts/787df708376a648ad511ac9013fe8b1738e06afb.jpg