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Missing values gwas analysis

SuperEla

Hello All,

I'm trying to run my GWAS analysis. When obtaining the results in chromosome 7, some missing values appear. I don't understand why it appears this way. Can someone help me?

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Chris_Kirchberg

Hi @SuperEla,

Are you using JMP Genomics or JMP Pro? Which version? Also, how are you running your GWAS analysis?

Thanks,

Chris_Kirchberg

Another thought I had a few seconds ago was the potential of missing data for those SNPs from that point on for each of your samples. Is the genotypes encoded numerically or other encoding?

SuperEla

Hello @Chris_Kirchberg,

Thank you for the quick reply. I'm using JMP Genomics 13.2. I ran the analysis through workflows > advanced > Genetic Q-K analysis workflow.

Let me know if that information helps.

SuperEla

@Chris_Kirchberg

The genotypes are numerical. I understand that there should not be any missing value since my annotation data set (map) has all the information for every chromosome.

Chris_Kirchberg

Thanks for the information. I that version number refers to the version of JMP that JMP Genomics is using. Did you get the number from the Help>About JMP option?

I am not sure why that workflow is giving missing values for your data set. It could be a few things like not enough non-missing genotype data for those SNPs (even though the annotation exists) or some other reason like missing values for Q or K information for those SNPs. Is it possible to share which settings you used for that workflow? Screenshots are good for each tab.

In this case, I think it might be best to contact support@jmp.com to see if they can help troubleshoot the source of the issues for that particular version of JMP Genomics.

SuperEla

I'm sorry, the version of JMP Genomics is 9.1.

Chris_Kirchberg

Thanks, that helps a lot. Let me check and get back to you to see if I can find a reason why before you contact support