Here the answers to my questions.
Thanks

- 
  Which are the main causes of background noise and how to correct it?

You will undoubtedly get a mix of high quality markers and low quality markers
and anything in between.
Some markers can be quite sensitive to reaction conditions, while others are
very robust. Slight inconsistencies between the different tips of a
multichannel pipette may cause markers to drop out and I even had some markes
that only worked at the edges of a 96 well plate due to minute differences in
PCR block temperature response between centre and edges! (i.e. column 1, column
12, row 1, and row 8 gave peaks while the rest of the wells did not).
Don't be scared by all this. Most markers will perform fine. If a markers is
suspect, just leave it out.

-    May the dye colour influence the magnitude of the background
noise?

Don't think so

-    How can protein / phenol contamination of the extracted DNA
affect
    AFLP quality?

Some people get the best results with DNA extracted with qiagen DNeasy kit. Also
phenol extracted DNA pellet diluted in H2O often works better than diluted in
TE (but the DNA will be less stable over long periods of time in water).

-    Is there any problem to overlay multiple primers with different
    dye labels? May peaks in one dye interfere with detection of
    other dyes?

Should be OK, but you will get spectral bleeding for the strongest peaks. They
(the real marker and the background peak) will give the same present-absent
pattern in and should be easy to identify.

Good luck
 
 
  

These
aren't elementary questions.  We are all still working to figure out the
best way to cut out noise from AFLPs.  I find running at least one pre-amp
and one selective amp (some people only run the selective amp) helps cut back
on some of the noise.  Also, make sure you set your threshold above the
noise.  (You can usually eye-ball that one.)  One last note on that
part: stick with larger peaks, as their less likely to be affected by things
other than your typical DNA. 

I don't know if dye color can affect the noise.  We don't have a lot of
money, so we only run one dye (and a different dye-ladder) at a time.  Hopefully
someone else can get back to you on that one.  I also don't know if the
different dyes can affect each other, but considering a lot of people use this
approach, I would like to assume any effect is minimal.

As for the protein/phenol contamination, typically it causes problems in
repeatability.  Therefore, make sure you run many of your samples multiple
times (the rule of thumb is 10%, but I typically run any of my
"trouble" samples multiple times) and discard bins where the peaks
are not replicable.

My favorite reference for florescently-labeled AFLPs is Meudt and Clarke 2007,
Almost forgotten or latest practice? AFLP applications, analyses and
advances.  Trends in Plant Science 12(3): 106-117.  Even though it is
a couple years old, it hits on most of the major questions to be considered
with AFLPs.  

Good luck!

Subject: Other: question about AFLP background noise

Dear all,

Maybe these are very elementary questions for this list, but I am
beginning with AFLP analysis and I have some doubts (probably elementary
ones as I said)

-    Which are the main causes of background noise and how to correct it?
-    May the dye colour influence the magnitude of the background noise?
-    How can protein / phenol contamination of the extracted DNA affect
     AFLP quality?
-    Is there any problem to overlay multiple primers with different
     dye labels? May peaks in one dye interfere with detection of
     other dyes?

Any references you could advice me to get into this subject and clarify
my doubts?

Thanks.

      

anidras_ayu@yahoo.com