Adjusting Settings

QTube's default settings are adequate for many applications, but you can adjust them to obtain results that may be more suitable for your particular application.  Use the ToolBar button [  ] or Settings->Preferences to access the preferences control panel.

General Preferences

These settings govern the way QTube computes fingerprints, and how sensitive the colors scales are.

If you change the settings, QTube will remember your new settings, even if you turn off your computer and come back tomorrow.  If you've gotten confused, please just press the "Restore Defaults" button to reset parameters to those shipped initially with QTube.


Resolution refers to the number of bins into which your FCS data are split in order to form Cytometric Fingerprints.  Higher resolution results in more bins.  This means that QTube can detect density changes in smaller locales within the mult-parameter space that comprises the fingerprints.

You can choose among three different resolutions. Lower resolution is appropriate when one or two dimensions are included in your fingerprints.  In general, higher resolution makes sense for larger numbers of parameters included in your fingerprint.  For example, if you include only CD45 and Side Scatter, low or medium resolution is probably the right choice.  If you add Forward Scatter, you may want to bump up the resolution one notch.  

Color Scale Limits

These values, one for each Metric, allow you to determine the mapping of colors to metric values.  The color scale maps metric values from 0.0 to the Color Scale Limit Value to the range of colors linearly shading from green, through yellow, to red.  Thus for example, if the Max Color Scale Limit is set to the default value of 3.0, and a tube metric is computed to be 1.5, the color for that metric for that tube will be yellow.  The value at which the limit is set is shown in the column heading for that metric in the Result Table.

Advance Preferences

Max Events * Parameters

QTube uses Cytometric Fingerprinting to arrive at its result.  Although QTube itself is pretty simple, the underlying technology is pretty sophisticated.  In particular, the computation of fingerprints needs quite a bit of memory.  To keep QTube from impacting other applications on your computer, we've limited its memory access.  If you find that QTube fails to produce a result you may need to limit the number of events it will use to compute fingerprints.

This number is determined by the product of the total number of events in the aggregate of FCS tubes times the number of parameters you request.  For example, if you add up all of the events and they sum to, say, 500,000, and you asked for CD45 and Side Scatter as the comparison parameters, the product of Events x Parameters is 1,000,000.  If you have a data set in which this product is larger than the maximum allowable, QTube will select at random a number of events from each FCS file that will keep the total within the maximum allowable (this is sampling your data instead of using all of it, which may not fit in memory).

If you find that QTube runs out of memory, try reducing Max Events * Parameters.  This will cause QTube to sample fewer events, thus allowing it to run even on large problems with limited memory.

Allow All Parameters

We really didn't want to include this as a choice, because generally it's the wrong thing to do.  QTube by default only allows you to compare only those parameters that are common across all tubes in a panel, because generally it doesn't make sense to compare distributions in which, for example, CD2-FITC is FL1 in one tube and CD19-FITC is FL1 in another tube.

QTube determines which parameters it will allow you to include in the fingerprint by examining the $PnN and $PnS fields in the FCS headers.  These both must match across all tubes in the panel for the parameter to be allowed.  However, if there is a mistake in one of your FCS headers, this checkbox will allow you to override QTube's default (and sensible) behavior.  If you've allowed all parameters and get a result that's mostly yellow and red, that's a good sign that it was the wrong thing to do.