Say I am doing RAPD PCR on some sample sets with 10 different primers, so that I will be generating 10 different binary matrices (based on presence or absence (as 0 and 1) of bands on electrophoresis gel).
I know the method to compute the similarity/distance coefficients (e.g. Jaccards distance) from a single binary matrix.
Now how do I calculate a single similarity/distance matrix pooling from all the binary matrices generated by individual primers ?
Please don't suggest me a software as I can do that with NTSYS PC. I want to know the actual statistical procedure behind.
Hello... RAPD is efficent to fast invistigation .
while I think you should apply the primer set to all samples.
the profile of DNA bands (fingerprint) contain the same loci (may I call them characters or traits). But if you used different primers the comparison will be not accurate.
Dear Kangkon Saikia
No need 10 similarity matrix.
order to profile bands, you can Arrange result of all prmers in one excel for analysis.
Dear Kangkon Saikia
Please, remember that RAPD detection of polymorphism based on the presence (dominant) or absence (recessive) of particular bands.
I do agree with Dr Mostafa opinion, arrangement results of all primers in one is an important step.
Wishes
Dear Kangkon saikia,
Agree with Dr Ziyadi, be note that, these are characters/traits considered to be inherited in Mendelian fashion.
Regards
Yes, I think that may be a good solution. But may i have any supporting reference.
And one thing more: what shall i do if i want to combine RAPD and ISSR result to create pooled dendrogram.
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