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.
Thank you very much for your response. Here it is:
Options in effect:
--file chr15
--pheno pheno.txt
--all-pheno
--linear
--covar CovSex.txt
--ci 0.95
--hide-covar
--missing-phenotype -9
--out chr15
19389 (of 19389) markers to be included from [ chr15.map ]
3152 individuals read from [ chr15.ped ]
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 3152 missing
1446 males, 1706 females, and 0 of unspecified sex
Reading alternate phenotype from [ pheno.txt ]
0 individuals with non-missing alternate phenotype
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 3152 missing
Reading 9 covariates from [ CovSex.txt ] with nonmissing values for 0 individuals
Before frequency and genotyping pruning, there are 19389 SNPs
3152 founders and 0 non-founders found
Total genotyping rate in remaining individuals is 0.978897
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 19389 SNPs
After filtering, 0 cases, 0 controls and 3152 missing
After filtering, 1446 males, 1706 females, and 0 of unspecified sex
Converting data to Individual-major format
Writing logistic model association results to [ chr15.P1.assoc.logistic ]
Reading alternate phenotype from [ pheno.txt ]
0 individuals with non-missing alternate phenotype
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 3152 missing
And the output from plink 1.9 is as follows:
19389 variants loaded from .bim file.
3152 people (1446 males, 1706 females) loaded from .fam.
0 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Error: No --covar values loaded.
Seems that plink doesn't find the phenotypes and covariate values to each of your individuals in the genotype file. Please make sure, that coding of IDs is consistent across ped and alternate phenotype as well as covariate files (lower/upper case is important here) and consider that any individual is denoted by two ID values: (i) family or pedigree id and (ii) individual id within family (exactly in this order). In addition make sure to use exactly one whitespace (blank or tab) as column delimiter in the phenotype and covariate files and remove quotation marks your software possibly intrudoces when saving the tables as text.
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