You can try to use the "Display transformation" option in FlowJo. See http://www.flowjo.com/v4/html/displaytransform.html for more detailed information. Basically, the scale is modified so that it is linear near zero, but maintains the log scale in the upper decades. More importantly for your question, it allows negative values to be displayed so that the cells you were not seeing now can be visualized in a nice symmetrical cluster. The above link goes into more detail, including displays comparing with and without transformation. Make sure that you read all of the documentation regarding using this, or you will get some 'interesting' results. The most important tidbit that I found was that you need to 'define transformation' using a data file that has all of the fluorochromes in your experiment (i.e. don't use single color controls for this). I suspect that this kind of display will begin to be utilized more and more in the future. Kevin L. Holmes, Ph.D. Chief, Flow Cytometry Section Research Technologies Branch Bldg. 4, Room B1-38 NIAID, NIH Phone: 301-496-9071 FAX: 301-402-4532 Email: kholmes@niaid.nih.gov -----Original Message----- From: Andy Johnson [mailto:andy@brc.ubc.ca] Sent: Wednesday, April 21, 2004 4:00 PM To: Cytometry Mailing List Subject: DiVa-FlowJo axis events As ever I will get more "out of office" replies, than true responses, but that seems to be the price to pay. I appreciate that the issue of DiVa data and events off the axis has been discussed thoroughly, but what are people doing about data presentation when they convert it to flow Jo ? It is possible to produce some nice plots in Flow Jo, but when you put quadrants on the plots you find that what appears to be "visibly" an empty quadrant has in fact 50% of the cells....all stacked up off the axis. The plots look fine in DiVa (some events on the axis), so what is the trick to getting flowJo and DiVa to look the same for publication purposes. We have been using flowJo for a long time and tried most of the tricks, but this is a constant issue that we cannot solve. Any ideas are much appreciated. Andy -- Andy Johnson FACS Facility Manager Biomedical Research Centre UBC Vancouver 604-822-7838Received on Fri Apr 23 17:38:00 2004
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