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: --all-pheno --allow-no-sex --bfile plink --ci 0.95 --covar plink.cov --covar-name rs1,rs2,rs3 --linear --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.)**