PCA with Plink1.9 - eigenval and eigenvec files are all 0

Question

[GiantSilverSoy]

Hi all,

I was trying to run pca using plink with the command:

plink --bfile array.data --pca --out array.data.pca

The resulting array.data.pca.eigenval and array.data.pca.eigenvec files are all in 0.

head array.data.pca.eigenval
0
0
0
0
0

head array.data.pca.eigenval
fid1 iid1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fid1 iid2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fid2 iid3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fid2 iid4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fid2 iid5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

There were no errors or warnings during the run.

Have anyone encountered this problem before?

Thanks!

Answer 1

[chrchang523]

Retry with plink 2.0; at minimum, it will print a relevant error message.

[GiantSilverSoy]

Thanks! The error said it was because of very-low-MAF variants.