Why do my dot plots appear sparse and blocky?

If your plot look like this, then you have a data file that has spurious low values. Some acquisition software, particularly BD FACSDiva, has a tendency to produce data files with events that represent noise, rather than real data. Note that there are data points in this plot with the value -7 million. Also note the clump of events in the far top-right corner: that is the real data.

A natural response when seeing data like this is to change the range that is being displayed on the plot, to only show the clump in the top-right. This is easy to do in FCS Express, using the Axis formatting category of the plot. In this example, because we are looking at linear parameters, set the lower range to be 0, and the upper range to be 262144.

However, after changing the resolution options, the result may look like this:

The reason that the plot now looks like this is that even though you change the range on the plot, FCS Express is still using the entire set of data in the file. The reason FCS Express does this is so that statistics calculated for each plot using a particular data file will give the same results, no matter what kind of visual changes you’ve made to a particular plot. Unfortunately, that means that the resolution that is used on the plot (typically 256×256 for a dot plot) is stretched over the entire range of data, from -7 million to 262144. You can see a more detailed discussion of the resolution issue in our Resolution Options Knowledgebase article.

For that reason, FCS Express also offers resolution options. In this case, it’s best to change 2 settings: the resolution options, so that the minimum value is 0 rather than automatic, and the axis range options, to set them back to automatic. After adjusting those 2 settings, the plot will again look like it is supposed to.