topic Re: Missing values gwas analysis in Discussions

Missing values gwas analysis

SuperEla — Fri, 09 Jun 2023 00:48:09 GMT

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?

Re: Missing values gwas analysis

Chris_Kirchberg — Mon, 18 Apr 2022 16:09:31 GMT

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

Chris_Kirchberg — Mon, 18 Apr 2022 16:12:27 GMT

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

SuperEla — Mon, 18 Apr 2022 16:24:51 GMT

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

SuperEla — Mon, 18 Apr 2022 16:41:29 GMT

@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

Chris_Kirchberg — Mon, 18 Apr 2022 17:04:25 GMT

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.

Re: Missing values gwas analysis

SuperEla — Mon, 18 Apr 2022 17:27:26 GMT

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

Re: Missing values gwas analysis

Chris_Kirchberg — Mon, 18 Apr 2022 17:30:59 GMT

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

Re: Missing values gwas analysis

SuperEla — Mon, 18 Apr 2022 17:36:40 GMT

Thank you! I really appreciate it.

Re: Missing values gwas analysis

Chris_Kirchberg — Mon, 18 Apr 2022 17:58:23 GMT

OK, I checked a data set I have with a few continuous traits and numeric genotypes. All of my SNP have some sort of result. It is not clear to me why yours show missing values. I have seen where some SNPs are excluded and do not have values, but there would be a column that would let you know which ones were excluded and I do not readily see that column in your results table.

I think now is a good time to contact support@jmp.com. Sorry I could not figure this one out for you.

Re: Missing values gwas analysis

SuperEla — Mon, 18 Apr 2022 18:10:02 GMT

Thank you so much! I will contact them!