Question: PLINK: missing covariates?
gravatar for spela.salamon
5 months ago by
spela.salamon0 wrote:

Greetings! I am trying to perform a linear regression analysis with SNP genotypes as covariates because i would like to assess the associations between phenotypes and combinations of SNPs. I have 11 SNPs in my binary files, and a bunch of phenotypes in my .pheno file. If i perform linear regression without covariates, or with various phenotypes as covariates, i have no problems and get sensical results. However, when i try to perform linear regression with SNP genotypes as covariates, i get a funny error. As you can probably guess i did not find a solution through google.

Here is the info (highlighted the lines that i don't get):

Options in effect:
  --bfile plink
  --ci 0.95
  --covar plink.cov
  --covar-name rs1,rs2,rs3
  --missing-phenotype 99999
  --pheno plink_pheno.pheno

11 variants loaded from .bim file.
519 people (220 males, 286 females, 13 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
313 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
--covar: 3 covariates loaded.
**519 people had missing value(s).**
Before main variant filters, 519 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.696269.
11 variants and 519 people pass filters and QC.
**Note: No phenotypes present.**
**Warning: Skipping --linear since # variables >= # samples.
(Check your covariates--all samples with at least one missing covariate are
excluded from this analysis.)**
plink linear regression • 484 views
ADD COMMENTlink modified 5 months ago by zx87549.1k • written 5 months ago by spela.salamon0

Can you post the first 10 lines of the plink.fam and plink.cov files?

ADD REPLYlink written 5 months ago by chrchang5236.7k
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