Hi @mjmg ,
Welcome to the community!
Fold Change and Log2 (fold change) are both difference measures (so equivalent to differences in the blog post) that ranges from negative to positive with a zero center. So that would go on the x-axis.when creating an volcano plot.
Although Volcano Plots are a statistical plot typically used for genomic data analysis visualization, it could be more generally applied to other data and industries. We wanted to generalize its application and to start from from a JMP Platform, like Response Screening, to get those differences and log (p-values) for a large set of data in order to make a volcano plot.
If you do not have fold change or log2(fold change) then you can use the Response Screening Platform to generate them. I would start with log2 of the data before using response screening. Then when you chose compare means, they will be the log2(fold change) values.
Does that help?
Ultimately, it does not matter where you get.generate the fold changes or p-values from. You can make the plot in JMP using graph builder.
Chris Kirchberg, M.S.2
Data Scientist, Life Sciences - Global Technical Enablement
JMP Statistical Discovery, LLC. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
www.jmp.com