Hi, I am transitioning from running microarray data in JMP Genomics to JMP Pro.
I routinely use the predefined JMP Genomics scripts such as:
Analytical Processes/Workflows/Basic/Basic Expression Workflow or
Analytical Processes/Expression/Normalization/Data Standardize procedures.
I was able to reproduce the STD normalization steps of the Normalization script but not the Basic Expression workflow.
One reason being because it is hard to identify all the steps used the analysis in order to calculate the same columns needed to create the volcano plots (example of data table attached from "View Data" output), cluster & heat map and PCA plots (attached screenshot). Another reason is that I find instructions to use "Response Screening" options of JMP Pro under "Analyze/Screening/Response Screening" or "Analyze/Fit Model/Personality: Response Screening" but none of them have all options available. The first gives the volcano plots but do not allow complex models and the second allow complex models (but not random variables) but don't give the volcano plots. Both of them show p-value cut-off of 0.01 and 0.05 for LogWorth but graphs are made only for p=0.01. Is there a way to change it to 0.05 or define another p-value? Is there a way to reproduce the same batch analysis included in the "Basic Expression Workflow" in JMP Pro?
