CmpSpots Program Frequently asked questions (FAQ)

The following are some frequently asked questions. This is a list of some of the questions that we will be answering. Please send us your questions about CmpSpots so we can add them and the answers to this list.

FAQ

How do I specify the two samples to pair? Through the -rsample: and -sample: command options.
What is a project and a project directory? What goes into this directory and can I have more than one? The project is where all of the input and output files are stored in your computer.
How do I change the options? If your are running the the -gui option (Graphical User Interface or GUI). Invoke the "Edit options" to edit the new parameters, then press "Pair spots" to re-pair the data with the new parameters.
What is a command line switch? How is it used? You specify the options to CmpSpots through command line switches. If you are running the GUI version, then you specify the command line switches through the Options Wizard window by pressing the Edit options button in the Report window.
How do I adjust the spot pairing parameters? Using the -gui option. Invoke the "Edit options" wizard to edit the new parameters, then press "Pair spots" to re-pair the data with the new parameters.
Can I save the options that I have just changed and apply them to other samples pairing operations? They are saved in the startup file "CmpSpots.properties" when you exit the program and are read when you start the program again.
How do I handle requiring different sizing parameters for different samples? Using the -gui option. Invoke the "Edit options" to edit the new parameters, then press "Pair spots" to re-pair the data with the new parameters.
How do I see the results of a spot pairing? When spot pairing is finished, invoke the "Image Viewer".
How do I stop the spot pairing program when it seems to have gotten stuck or is taking too long? Press the "Stop pairing" button.
How do I generate an XML output file? The default is to use the "-spfFormat:X" switch.

Contact us CmpSpots is a contributed program available at open2dprot.sourceforge.net/CmpSpots Revised: 10/04/2005