Volcano Plot parameters in JMP ProWe don't have JMP Clinical or Genomic so we're using JMP Pro to create a volcano plot according to this article:
How to Build a Volcano Plot in JMP!
Most volcano plot differences refer to the x-axis as fold change or log2(fold change). The terminology in the article uses Difference. It also indicated to use Difference only as opposed to Relative Practical Difference.
In the wiki article on fold change, there is also a reference to relative change.
In JMP context, how do all these terms relate to fold change or log2(fold change)?
OtherRe: Volcano Plot parameters in JMP ProHi @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.
Re: Volcano Plot parameters in JMP Pro@chris_kirchberg thanks for some of the efforts in making volcano plots more mainstream, I'm still a bit confused with the terminology. Hopefully your team can make the generation of volcano plots more streamlined or better explained.
Mainly I need to find the direction of the data generated by JMP volcano plot (whether it is ControlGroup-NotControlGroup or NotControlGroup-ControlGroup; is ControlGroup on the left or on the right side, etc...), set up fold change or differences thresholds in the x-axis that would be comparable to published references (x1 or x2 fold change or log2(fold change) = +/-1). The explanation is not that clear from the tutorial when the term Differences is used and is it equivalent to Fold Change or log2(Fold Change)?.
My data is not log2 transformed, but I'm working on normalized (against a reference), centered and autoscaled data. So it is better to have log2 transform on my data even if its normalized, centered and autoscaled already and include log2 transform in the preprocessing process so the Difference parameter is directly equivalent to log2 Fold Change?
