Hi, I'm trying to do a CCA, using PAST3, of two phylotypes in 7 samples to analyze the relationship with 8 to 12 environmental variables. These phylotypes are from a certain molecular marker. A problem is that the designated PCR primers also amplified two types sequences totally unrelated to my molecular marker, yet they make about 50% of the total clones. The situation is that if I use only the correct phylotypes in a CCA, I get that all variables are in one axis, thus making the CCA analysis useless. If I add the other two unrelated "phylotypes", I get a CCA plot that makes sense: but I doubt it is right and representative about the relationship of the environmental variables and the "correct" marker phylotypes. Can I really use the 2 correct phylotypes of my gene in combination with the 2 unrelated-to-my-gene "phylotypes"?
If not, I'm looking for alternatives for software or multivariate analyses. I'm using PCA with the environmental variables and the Simpson index, so in the biplot, the Simspon index is a variable, but I've no idea if I'm doing it right. Please help me.
Edited by Procyon, 15 June 2014 - 05:17 PM.