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

[#1]

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

[#2 · Accepted solution]

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,

[#3]

Hi Chris,

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

Thank you!

Liu