Entering edit mode
8.9 years ago
anikduttapotol
▴
10
Hello,
I have done a principal component analysis based on 250 SNPs from a single locus of 100 diploid individuals. The eigen value of the first two principal component describe more than 40% variation. But the problem is I do not have any population information. So the pca plot only shows the dots. So how can interpret the result? Please suggest me how to do that.
Why did you do the PCA? That is, what question are you trying to answer with your 250 snps and 100 individuals?
I am trying to see if there is any genetic similarity between the individual, I also want to check if there is any effect of evolution or geographic distribution.
So do you have the geographical data?
You can combine your data with individual 1000G genotype data (individual 1000G genotype data) and run the PCA again. But 250SNPs from a single locus could be to small to separate the individuals correctly.