This JMP Add-in is to transform non-normal quantitative trait data typically analyzed in Genome Wide Association Studies (GWAS). The method implemented is rank-based inverse normal transformation (INT).
A simple interface is create to choose the traits to be transformed and then clicking OK to create new transformed columns (see screen shot below).
The output is two sets of columns: 1) _INT as a suffix. These are the transformed trait values 2) _p as a suffix. These are the probability values of the transformed columns.
There is a paper that discusses INT and its different forms. It also can be used to provide guidance.
McCaw ZR, Lane JM, Saxena R, Redline S, Lin X. Operating characteristics of the rank-based inverse normal transformation for quantitative trait analysis in genome-wide association studies. Biometrics. 020;76:1262–1272.
https://doi.org/10.1111/biom.13214
If there is interest, additional methods could be incorporated and the window can be updated to allow choosing these methods.
UPDATE: Now version 2 of the add-in includes the below:
- Added option to include or not include probabilities
- Added an option to choose between Arbitrary or Average when there is a tie. Tie method chosen will write a note to the data table as to which method was used.
This add-in was created on, for and tested in JMP/JMP Pro 17 and JMP/JMP Pro 18