Cheers All,
I'm studying the genetic diversity of a rare plant using AFLPs as the
molecular marker. I'm planning to use the scanAFLP method as a
semi-automated means to score my data. My goal is to bring as much
objectivity into the scoring process as possible.
The authors of this method used GeneMapper to produce a "sum of signal".
Thisis a normalization option in GeneMapper that "sums up the signals
within the analyzed range for each sample and calculates the average
over all samples." I don't have access to GeneMapper, but I do have the
option to use GeneMarker.
Unfortunately, manipulating GeneMarker is not entirely straightforward
and I've struggled trying to interpret portions of the user's manual.
I'm wondering if anyone has experience with this program and may be able
to give advice on two things:
1) Is there an option in GeneMarker to produce a sum of signal as is
available in GeneMapper?
2) I have also struggled to calibrate the Run Wizard settings in
GeneMarker in such a way that the automatic scoring function accurately
scores alleles based off of a manual panel that I create. This program
seems to dismiss (or score as 0 / not present) alleles that appear
obviously present to me.
If anyone might be able to provide further insight about any of this,
I'm very interested and appreciative!
Many thanks,
Wendy McBride
wm...@nau.edu <mailto:wm...@nau.edu>
