Question: PLINK: missing covariates?
gravatar for spela.salamon
15 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 • 1.2k views
ADD COMMENTlink modified 15 months ago by zx87549.9k • written 15 months ago by spela.salamon0

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

ADD REPLYlink written 15 months ago by chrchang5237.6k

I'm also facing the same error. I just have 10 samples. What will be the reason for this error? could you please help me out?

Thanks, Karthick

ADD REPLYlink written 8 months ago by karthick.n10

As I noted at , you don't have enough samples. See e.g. .

ADD REPLYlink written 8 months ago by chrchang5237.6k
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