AttachParameters

Attaching Data

Data can be important from text files in CSV format and attached as additional parameters to FACS data files. The attached parameters are treated like derived parameters - the can be shown like all parameters, transformations for displaying them are possible, and statistics calculated. Bit attached parameters are not used for the spill-over matrix and compensation. (Well, wouldn't make sense, would it?)
So why would you want to do that? For example, you might calculate clustering in a different program, export the cluster asignment for each event and import it here for further analysis.

In the dialog "Data Files - Attach Parameters" dialog, the data can be imported and attched (and removed) as new parameters. The relevant FACS data file can be selected in the file list on the last.

Organizing attached data

On the "Show Parameters" tab, the currently attached parameters are shown - and can be deleted. Please note: deleting a parameter can change regions and how plots are shown. Be careful and control your regions, gates and plots

Importing data

On the "Import Parameters" tab, external text files can be imported as additional parameters. "Open" the text file and the file is analysed and shown. In general, the text file has to have one line for each event. Each line contains all parameter values for that event. The first line can be a header line, which will be used to provide labels for the parameters.
For example:

Param1, Param2, Param3
10.0, 100.0, 1000.0
100.5,100.0,10.0

This file would have a header line and two events; each event has three parameter.
You may have to define the format of the text file:

Option	Explanation
First line as parameter name	The first line will be used to define the parameter label. This is 'on' by default.
Parameter separator	This is the character separating the values on one line. The default separator is 'tabulator'. (For the example above, it would be ','.)
Decimal point indicator	How is the decimal point defined in the file - ist it a '.' or a ','? '.' is the default option. (The above example also uses '.')

The data table shows all data in the text file, as well as options for importing.

Option	Explanation
Name	Enter the name that shall be used for the new imported parameter. The name can't be empty. If the data file contains a header line (see above), th name is poulated from there.
Import	Check this box if the parameter shall be imported.
Event#	Check this box if this parameter is actually the number of the event for which the values shall be imported. This is usefull if your imported data covers only some specific events in the FCS datafile, not all events. For example, you might have exported only the events showing in a particular (gated) plot, used that data for generating additional data (like a cluster number), and are now adding that data to the events used in the export. All other events will get the value specified under for #missing Please note: the Event# must be sorted in ascending order!
Log Display	Shall this parameter be shown on a log-scale by default? This can always be changed later under "Transformation" - it's just for convenience.
Categorical	Is this a category instead of a measurement? Categories can be defined in the original TXT/CSV file either as a number or as a text. When importing, FCSalyzer changes the category information into equally spaced values. For example, if the text 'female' and 'male' are used to define categories, they will be changed to 100 and 200, respectively. Similarly, the values 0, 2, 5 will be changed to 100, 200, 300. If there are missing values, an additional category will be made that holds all those events. When displaying that parameter in a plot, the plot axis will not show the regular ticks based on values, but instead custom ticks that show the category, for example '[male]' or '[0]'; the category that holds events with missing values will be in the category '[]'.
Jitter	During importing, a small random change will be applied to the values ('jitter'). This jitter is useful when importing categories, as then the values will not be precisely '100' but somewhat around that value, turning them into a nice visible population instead of just one single point in the plots.
Range	This value defines the maximum range of the parameter, and will thus define the display range of this parameter in the plots. The value can be adjusted by you, but not be set lower than the highest value.
Highest Value	For your information, this is the highest value that was found for this parameter.
Status	For your information: are there non/numerical values found for this parameter? Are there values for all events of the selected FCS datafile (file list to the left), or are there values missing?
for #missing#	If values are missing for events, this value will be used instead. It is better to prepare values for all events instead of relying on this replacement value.

When clicking on 'Import', the selected values will be imported and attached as additional parameters.

Saving attached data

Attached data will be stored in one combined data file with the same name as the main document, but the ending '.FCXA'.

Please note that this data file contains also the name of the parameter (see above), which can be easily extracted from the .FCXA file using common file readers. Also, as FCSalyzer is a freeware open source program, anyone can analyse how the data is stored in the .FCXA data file.

Please make sure that the .FCXA file contains only information as permitted by your organization.