This video shows how to set up, run, and interpret a basic expression analysis in JMP Genomics. In this example I use the Basic RNAseq Workflow, which is a pipeline of some simple exploration on the markers and samples (looking at expression distributions for samples, removing "bad" samples, normalizing the samples' expression, exploring correlations and principle variance components) directly into an ANOVA analysis on the log2(expression) to find markers that are statistically significantly differentially expressed. We explore the resulting output as volcano plots (which we can filter further), Venn Diagrams to find markers significant in multiple comparisons, and tables of information about the final set of selected significant markers.
This analysis can apply to any kind of continuous data across any kind of biological markers, such as metabolomics, proteomics, or expression.
