Entering edit mode
7.4 years ago
aritra90 ▴ 70
Hi, the CONVERTF program in EIGENSOFT package is ignoring few samples and not calculating their principal components.
I am seeing this in my terminal when executing CONVERTF.
genetic distance set from physical distance Sample1 ignored Sample2 ignored Sample3 ignored ..................... Samplen ignored genotype file processed numvalidind: 21 maxmiss: 21001 packedancestrymap output ##end of convertf run
Usually, it says ignoring all samples and then outputs the principal components for all the samples. I am just inputting the .PED and .MAP files in par.PED.EIGENSTRAT. It'd be great if anybody can give me some insight on this.
Yes, I saw the same just right after posting :P
Thanks, Philipp, it works now!
Although the answer says that "Try setting column 6 to 1." I assume that it does not influence PCA results at all?
If I remember correctly, that column is reserved for phenotypes, which are not used in the PCA