479862_en-US

liliconcom

Missing values gwas analysis

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?

 

 

AnalyticsWindowsRe: Missing values gwas analysis

Hi @SuperEla,

 

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

Thanks, 

Re: Missing values gwas analysis

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?

Re: Missing values gwas analysis

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.

Re: Missing values gwas analysis

@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.

Re: Missing values gwas analysis

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.