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Fers
Community Trekker

SNP-Trait Association

I have a population ~4k individuals genotyped with ~40k SNPs. My phenotype is a binary trait. Most individuals have score 0 and only nine individuals have score 1, and 41 missing values. I am trying to fit also 6 covariates as random effects by using SNP-Trait Association option in JMP Genomics. I am getting the following error message.

 

ERROR: PROC GLIMMIX generated no estimates for the Genotype Test for trait Shredded. There may be excessive missing data or the contrast may be nonestimable. Please see the log for more details.

 

Does the algorithm allow for missing values?

 

Thanks

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4 REPLIES 4

Re: SNP-Trait Association

@Fers ,

 

Where are the missing values? Mainly for a few samples or in for a few genotypes?  SNP-Trait Association will drop samples/genotypes that have missing values.  You might want to run Marker Properties to find the missing propotion of Genotypes and Samples and then filter Samples/Genotypes by reducing this number.

 

Also, you might want to connect with support@jmp.com to help find if this is due to the missing values being related to being found in the rare trait or one of the covariates.

 

You can also explore this using JMP's distribution platform under Analysis or use the Marker Properties process in JMP Genomics to isolate the missing values and then look at the distribution of the samples/markers relatives to the trait/covariates.

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com
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Re: SNP-Trait Association

@Fers,

 

Another thought is that if those markers and samples need to be there, you can impute the genotype using nearest neighbors. In JMP Genomics 9 this process was added and can be found under Genetics Utilities. This might be helpful given the proportion of missing genotypes is small relative to the total number of genotypes.  Also to consider, are these missing values due to array or sequencing errors? Or do they hold some special meaning (not enought information, to variable to call, etc.)?

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com
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Fers
Community Trekker

Re: SNP-Trait Association

The genotypic data is already imputed, so missing is not an issue. But I have aroud 45 samples with missing phenotype. I already tried by removing the samples with missing values and it seems I have other troubles.

 

ERROR: PROC GLIMMIX generated no estimates for the Genotype Test for trait Shr

 

Thanks

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Re: SNP-Trait Association

HI @Fers ,

 

I would contact support@jmp.com at this point and they should be able to help troubleshoot why you are still getting an error.  Please let them know you are using JMP Genomics, which version and your site number so they can make sure you get to the correct person.

 

Sorry I could not be more help.

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com
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