topic Re: How to make differential gene expression volcano plot using means difference in response screening in Discussions

How to make differential gene expression volcano plot using means difference in response screening

xliu — Tue, 21 May 2024 01:25:00 GMT

Dear experts,

I'm trying to make a differential gene volcano plot showing the means difference with JMP17.2. I used response screening and set a control using the column info, but I couldn't find where to apply the "means difference" option. The graphs I got so far just have FDR logworth by effect size, by Rsqured, or by Slope, I couldn't get FDR logworth by means difference. And the in Result table, I also could not see the "means difference". I followed the JMP Academic: Genomics Research in JMP Pro YouTube, but it didn't show how the means difference was obtained.

Can someone let me know how to solve this issue? Thanks a lot!

Liu

Re: How to make differential gene expression volcano plot using means difference in response screening

Chris_Kirchberg — Tue, 21 May 2024 14:35:08 GMT

Hi @xliu,

There are two ways to get the Volcano plot and the Mean Differences table to show when using Response Screening from Analyze>Screening>Response Screening:

In the dialog box before running Response Screening, you can check the box Common Y Scale. This assumes that all of the Responses are normalized to the same scale.

Go to the Red Triangle in the Report and choose Show Means Differences

You will be prompted in a window that looks like below. Click on Continute

You will now have the Volcano plot as the last tab and the means difference table below.

Hope that helps,

Re: How to make differential gene expression volcano plot using means difference in response screening

xliu — Wed, 22 May 2024 05:37:42 GMT

Hi Chris,

Thanks a lot for the help! It was helpful. I could generate the volcano plot with means difference now.

Thank you!

Liu