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Does anyone know how to get variables in each of PC1, PC2, PC2 in PCA?

Thank you.
Load your data set into JMP, then run the Principal Components Analysis from the main menu, i.e. Analyze | Multivariate Methods | Principal Components. You'll get an output that initially shows a scree plot, but you can expand that to show scores and loadings plots among other options by clicking on the "Principal Components / Factor Analysis" bar. At the bottom of that options list you'll find "Save Principal Components". If you click on that, you'll be asked how many components you want to save. Answering that question will append that number of principal components onto the right of your original data table: they'll be called "Prin1", "Prin2" etc - from where you can save them, import them into other analyses etc.
Hi David Q/R,

Thank you for your reply.

Unfortunately, I still cannot find the way to do it...

I am analyzing a microarray data. I first upload the data for normalization, then, I look at PCA to see how my samples are grouped. Specifically, I'd like to know which probes are involved in the principal component 3, along which my samples separated into 2 groups.
When I open the data correlation result, I do not even see principal component/factor analysis bar...

I appreciate your help!

Community Manager


Jun 23, 2011

Hi Sy,

What version of JMP are you using?

Hi Jeff,

I am using JMP Genomics 5 (JMP 9).


Jun 23, 2011

You want to run a different process to obtain this information.

Try "Principal Components Analysis" under the Pattern Discovery section of the Genomics Starter. This will enable you to look at the PCA results for samples and genes simultaneously.