Hello everyone,
I would like to count the PCoA in Genlaex for my AFLP matrix (it is from GeneMarker, binary- 0/1). I have 672 samples, 55 populations, with different number of samples in populations and 360 alleles (3 combination of AFLP selective primers) . I have tried to change the matrix as it should be, based on the genalex instructions but still I have some errors, but I can't find them. I get an information that there is a problem with the matrix and I should check it. I try, but still I don't know what is wrong. Does anyone know how this matrix should look like?
Dear Justyna,
Genalex cannot deal with dominant marker such as AFLP into PCoA analysis directly.
You should transformed it into distance matrix before conducting PCoA analysis.
You can calculate pairwise distance in GenAlex to help you obtaining distance tri-matrix and subsequently you can conduct PCoA through the matrix instead of genotyping data of AFLP.
Thank You, Bing-Hong Huang :)
They should correct the instruction, because there is an information that this software work with big data set for examples from AFLP ;)
I try FAMD, but when I think that I will have to color all this circles I decide to find something better and I still looking ;)
Hi Justyna,
I am not sure if you are still looking for software which will be useful in your experiment. If GeneAlex seems to be a trouble for you, I can recommend PAST software:
https://folk.uio.no/ohammer/past/
You can work directly on your binary data without the need of distance matrix calculation - PAST does it for you. You can choose different ways to analyze your data including PCA and PCoA.
Good luck
Piotr
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