04 April 2015 4 2K Report

I am trying to run the linear association analysis with a separate phenotypic file where I have 12 quantitative phenotypes. When I try to run the analysis I get the message that I have 0 cases and 0 controls and 3000 missing cases. My ped file has its 6th (phenotypic column) coded as -9. Does anyone knows how to fix this problem? I am using Plink 1.7 for this. If I try doing the same thing with the Plink 1.9 version I get 3000 '0 phenotype values present after --pheno' messages. 

This is the command that I have been using:  

./plink --file chr15 --pheno Pheno.txt --all-pheno --linear --covar CovSex.txt --ci 0.95 --hide-covar --missing-phenotype -9 --out chr15 

Thank you in advance.

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