Knowledge Base: How do I display my data in FCS Express as it appears in Summit software?

How do I display my data in FCS Express as it appears in Summit Software?

FCS files in Summit software are displayed on a 0-256 linear or 0-100,000 logarithmic scale. However, the data are stored within the data files as 32 bit, with a range of 0-4,294,967,295. When the data file is viewed in FCS Express with default preferences, the 32 bit native values are displayed on the axes and used for subsequent calculations. The resulting plots may appear different than originally displayed in Summit software due to the different scales, and statistics (means and medians) will be based on the native values.

However, the preferences in FCS Express 6 may be easily changed to scale and view the data as displayed in Summit software via the instructions below.

To rescale Summit data in FCS Express 4 or 5, please see the section on Rescaling Summit Data in previous versions of FCS Express.

How to rescale Summit data in V6 (after 6.004.0034 release)

To have FCS Express scale your data identically to Summit software automatically you will need to adjust your FCS Express User Options via the steps below (please see image below for reference):

  1. Select the File Tab > Options.
  2. Expand Data Loading Options.
  3. Choose FCS File Options.
  4. Check the box next to Scale Summit/ZE5/S3 log parameters.
  5. Open the Scale Summit/ZE5/S3 lin parameters drop down and choose a value to use for the linear parameter range.
  6. Click OK.

Your user preferences will now be set to scale Summit data as seen in the Summit software anytime a file is loaded. These changes will only need to be done once for each user.

FCS Express User Options - Changing FCS File Options to Automatically Scale Summit Data

 

The change in preferences will result in data loaded in FCS Express as it was displayed in Summit Software. The images below show the same data set scaled with the FCS Express default options (top) and with the scaling settings updated (below).

Plots in top row use default settings, while plots in bottom row use new scaling options. Linear parameters are displayed on left plots, and logarithmic parameters are displayed on right plots.

 

 

How to rescale Summit data in older versions of FCS Express (Version 5 and Version 4)

There are two options for rescaling or displaying the data in FCS Express

  1. Use the Divide by Axis Labels feature: Using the Divide by Axis Label feature will display the axis as they are seen in Summit but will not change the native raw data or statistical values.
  2. Use the Parameter Math Feature: Using Parameter Math will create a new parameter based on the scaling factor. The native raw data values will also be scaled accordingly.

Using the Divide by Axis Labels Feature

The Divide by Axis Labels feature may be accessed by right clicking on a plot>choose Format>Axis Category>Divide By Factor. Using the Divide by Axis Labels feature will display the axes as they are seen in Summit but will not change the native raw data or statistical values.

For Linear Parameters type the value 16777216 into the Factor box.

 

For Logarithmic (fluorescence) Parameters type the value 42949.67296 in the Factor box.

 

Once values have been entered, click OK. Below is an example of the data before and after making the Divide by Axis Labels change.

Summit data before applying the Divide By Axis labels change. Summit Data after applying the Divide By Axis labels change. Notice the Axis values have been updated according to the scaling factor but the X and Y Median values have not changed.

 

Using the Parameter Math Feature

The Parameter Math feature may be accessed in the Transformation Navigator from the Tools tab>Transformations>Transformations command. More detailed information about setting up parameter math can be found in our Using Parameter Math Manual Topic. Using the Parameter Math feature will create new parameters based on the scaling factor resulting in parameters that are displayed on the correct scale and raw data values that reflect the scaling change.

In Transformations navigator, create new parameter math and click New below Formula Sequence box to add sequence for linear parameter. The Create New Sequence Item dialog will appear. Enter formula as depicted in image below and click OK.

For Linear Parameters use the scaling factor of 16777216 to divide the parameter number by. In the example below SSC-A is represented by P8 so the resulting formula is: =P8/16777216.

In Transformations navigator,click New below Formula Sequence box to add new sequence for logarithmic parameter. The Create New Sequence Item dialog will appear. Enter formula as depicted in image below and click OK.

Once parameter math formula sequences have been defined, click and drag the newly created parameter math from the Transformation navigator to the plot. Below is an example of the data before and after performing parameter math on the data. Please note that you may also overwrite the original parameter by choosing it from the Output Parameter drop down in the Create New Sequence Item dialog. Once applied, the new parameters will be available from the x- and y- axis drop down lists on the plot, and "Parameter Math applied" will be appended to the plot title.

Summit data before applying performing parameter math on the data. Summit Data after performing parameter math. Notice the Axis values have been updated according to the scaling factor and the X and Y Median values have changed to reflect the newly created parameters.