[GenABEL-dev] No COVAR variable in output when using --robust with the --mmscore option

[L.C. Karssen]

Dear Jennifer,

Thanks for your interest in ProbABEL. We are trying to concentrate our
user support effort on our forum, so please post your question there.
The GenABEL forum can be found at http://forum.genabel.org. With more
eyes looking at your question I expect a much faster answer there. 


Best regards,

Lennart Karssen.

On Thu, 2011-06-09 at 13:26 -0400, Bragg-Gresham, Jennifer wrote:
> Hello,
> 
>  
> 
> I am trying to use the palinear software to run GWAS with
> genotype*covariate interactions and I have family pedigree to account
> for. I have the software running with the –mmscore function and with
> the –robust function, but I am not getting the COVAR_SNP_INT variable
> in my output files. I can get them if I remove the –mmscore function,
> but that is not helpful, obviously. I am wondering if this a bug in
> the program or if there is something else I need to do.
> 
>  
> 
> Here is my command line:
> 
>  
> 
> runon $bin/palinear --pheno $pheno/${trt}1a2_${who}.txt --dose
> $pheno/doses/$i.mldose.gz  --info .temp.$i.mlinfo --interaction=1
> --robust --mmscore $pheno/InvVarCov_matrix_${trt}1a2_${who} --out
> $pheno/MODEL2/$who.$trt.$i > $pheno.$who.$trt.$i.log
> 
>  
> 
> Thank you for any assistance you can provide,
> 
>  
> 
> Jennifer
> 
>  
> 
> -- 
> 
> Jennifer L. Bragg-Gresham, MS
> 
> Center for Statistical Genetics
> 
> Department of Biostatistics
> 
> University of Michigan
> 
> 1415 Washington Heights
> 
> Ann Arbor, MI 48109-2029
> 
>  
> 
> Phone: (734) 763-2161
> 
> Fax: (734) 615-8322
> 
>  
> 
> Office: 4622 SPH I
> 
> E-mail: jennb at umich.edu
> 
>  
> 
> 
> _______________________________________________
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> genabel-devel at lists.r-forge.r-project.org
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-- 
-----------------------------------------------
L.C. Karssen
Erasmus MC
Department of Epidemiology
Room Ee 2224

Postbus 2040
3000 CA Rotterdam
The Netherlands

phone: +31-10-7044217
fax: +31-10-7044657
e-mail: l.karssen at erasmusmc.nl
GPG key ID: 0E1D39E3
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