PCA troubles

PCA troubles

0

Hello everyone!
I’m trying to project my ancient sample on PCA with 2 different basis: simons data and 1000. I am using smartpca from admixtools and eigenstrat files as input (exclude outliers). Something strange occurred, the ancient genome and its downsampling versions (cucrled) laid far away from each other and the main fork. Furthermore, if we use simons dataset as the basis the PCA plot looks different. Could you tell me why this can happen and how to fix this?

1000Genome + ancient sample
Simons dataset + ancient sample


dataset


genomes


smartpca


pca


admixtools


simons


1000

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