General FAQs

General Frequently-asked questions

How long does FAST-MAP takes?
[4/21/97]

It depends very much on the following factors:

The speed of your computer;
The memory available for your computer (using virtual memory on a Macintosh may slow down processing because of swapping time);
The network and user load if you are running FAST-MAP on a multi-user host machine;
The size of the gel:
- the number of loaded lanes,
- the number of markers in the panel
The data quality of the gel: the cleaner the gel, the faster FAST-MAP will be;
If it is a new marker panel, FAST-MAP will take longer because of a steper learning curve.

On our UNIX (multi-user, HP) workstation, it normally takes about two to three hours on a typical gel with 32 lanes and 15 markers. This is after minimal hands-on time. This is where FAST-MAP uses the most time:

prep_call or image extraction takes about 3 to 10 minutes;
image_call or lane/size tracking takes about 5 to 15 minutes;
quantitating takes about 4 to 10 seconds per experiment;
genotyping takes about 2 to 5 seconds per experiment.

However, your mileage may vary.

What is the importance of a study vs calling gels individually?
[4/21/97]

It is advantageous to use a study to bundle related gels together. This is especially so when genotyping a marker panel for the first time .
In a study, allele binning is done across all the gels, as well as the initial stutter pattern learning. If you call the gels individually, then the allele binning and the stutter pattern learning are done incrementally and may be inconsistent from one gel to another.

How good is data from the first time you use a new marker since there
is no stutter pattern established? 
[4/21/97]

It depends on

how good the data are; and
how much data are available.

Usually, an initial study of 2 to 3 good quality gels is sufficient to get FAST-MAP going.

What do those criptic symbols in the allele_call traces mean?
[4/21/97]

They are for the FAST-MAP developers to keep track of the various stages of FAST-MAP's progress. For example:

   Quantitating lane 5...a.b.a.b.....Done.

Each "a." means the start of the global optimization routine and each "b." means the end of an optimization iteration. If there were too many "a.b.", it means possibly noise in that lane so FAST-MAP was having trouble with that epxeriment.

There are also many "cryptic symbols" in "image_call", for example:

   Scanning for gel lanes.......___+++++.::::Done.

Each ".", "_", "+", and ":" has its own internal meaning. In general, each "+" means FAST-MAP was trying out a certain hypothesis (with the best guess first). So, if there were many "+"s, it is a warning sign that FAST-MAP was having trouble performing the lane tracking and you may want to abort the execution and check the "layout" and perhaps use "image_view" "Draw" mode to help FAST-MAP.

We will give a more detailed description of these cryptic symbols if there is more interest. For now, it is safe to ignore the symbols or treat them as a signs that the computer is still working on the gel.

How do I turn off the help messages when starting up FAST-MAP?
[4/21/97]

Edit your "startup.m", go to the section labeled "Step 2" and change "HELP_ME=1;" to "HELP_ME=0;".

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