Eigenvalue and eigenvector files from pca equal to zero

[Irene Villa Machío]

Hi all!

I'm trying to calculate a pca with my data but I get eigenvalue and eigenvectors files that are equal to zero.

First, I have pruned my matrix with the command:

plink --vcf $VCF --double-id --allow-extra-chr \
--set-missing-var-ids @:# \
--indep-pairwise 50 10 0.1 --out out

And I get the correct files. Then, I type for  pca:

plink --vcf $VCF --double-id --allow-extra-chr --set-missing-var-ids @:# \
--extract out.prune.in \
--make-bed --pca --out out_80md

Log file:

PLINK v1.90p 64-bit (16 Jun 2020)              www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to out_80md.log.
Options in effect:
  --allow-extra-chr
  --double-id
  --extract out.prune.in
  --out out_80md
  --recode vcf
  --set-missing-var-ids @:#
  --vcf out.vcf

8192 MB RAM detected; reserving 4096 MB for main workspace.
--vcf: out_80md-temporary.bed + out_80md-temporary.bim +
out_80md-temporary.fam written.
7761 variants loaded from .bim file.
7761 missing IDs set.
79 people (0 males, 0 females, 79 ambiguous) loaded from .fam.
Ambiguous sex IDs written to out_80md.nosex .
--extract: 2277 variants remaining.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 79 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.875975.
2277 variants and 79 people pass filters and QC.
Note: No phenotypes present.
--recode vcf to out_80md.vcf ... done.

I don't get any error, however, my files are zeros.

Does anybody have an idea what is wrong? Any help would be appreciated.

Thank you!

Irene

[Christopher Chang]

Try rerunning with plink 2.0; it is more likely to provide a useful error message.

[Irene Villa Machío]

Hi,

I had samples with a high level of missing data (or empty). So this was the problem.

I removed them from the matrix and now the pca files have information.

Thank you for your response.

Irene