This case study focuses on how to use JMP Pro 17 for 'omic data analysis, specifically marker assisted breed/genomic selection data. It primarily looks at exploration of markers and traits of Loblolly Pine Trees and adds predictive modeling to then simulate progeny/offspring to see which crosses/matings between parents are likely to give the best desired traits. This type of analysis is typical of Breeders and Statistical Geneticists of Breed programs in Agriculture (Crop and Animal Sciences)
This case study can be used to give demos to customers by SEs for those interested in analyzing 'omic data in the clinical research space. It is designed so that you can show only the capabilities that are requested by the customer (use Great Demo! method) but also in context to the whole analytic workflow of analyzing this kind of data. If you do try to demo all of the capabilities, it will take you over an hour since there are many capabilities that are used.
The included journal contains script buttons to perform the analysis at each step. There are also script buttons that perform some data manipulation tasks as well. Some of the analyses can take a very long time so best to pre-run them before giving a demo on them.
The Venn Diagram add-in could also be used.
What's Available:
- A JMP Journal with an introduction to the workflow, the scientific/research question, and the data set used
- JMP Data Table
- The data set(s) so you can create the JMP Data Table
- Paper referenced in Journal
Why is this useful?
- JMP Genomics as a product was discontinued earlier this year so we need case studies to show how to perform 'omic analysis in JMP Pro 17
- It also highlights what is new in JMP/JMP Pro 17 for wide data, especially in the context of 'omic data
- It additionally is meant to help SEs become more self-sufficient in given demos and talking about capabilities in the 'omic space
- Data analysis in the 'omic world can be scripted/workflow oriented or exploratory in nature. This case study will focus on the more exploratory nature of data analysis and not the "automated" or scripted type analysis. One can convert the steps into a workflow using JMP Pro 17's workflow building capabilities.
