PLINK linear regression unwarranted error message?

Question

[dam4l]

Hi,

I am trying to run a GWAS with a quantitative phenotype in PLINK. I'm using linear regression with principal components from population structure analysis as covariates. The command is as follows:

plink --bfile genotypefile --pheno pheno.txt --allow-no-sex --covar covariates --covar-name PC1,PC2,PC3,PC4 --out gwas_results --linear hide-covar --adjust

The log file says that there are 0 phenotype values present after --pheno and I have received the following error:

--linear without --all-pheno requires a scalar phenotype

I am not sure how this could be because my phenotype is scalar and I have conducted GWAS with this same sample and a very similar phenotype with the same file format without issue. The phenotype file is in a .txt document that looks like this:

FID     IID     pheno
0002    0002    10.18651
0005    0005    31.99052
0007    0007    44.79303
0081    0081    39.33981
0082    0082    -15.43773
0083    0083    31.8429
0088    0088    -18.39446

I'm not sure what I can do to resolve this issue. Any input would be greatly appreciated.

Answer 1

[chrchang523]

Check whether the FID/IID values in pheno.txt match those in your .fam file.