i have a huge RNAseq data set (read counts) and i just want to transform the reads into different styles. Ofc I know that the best software for this might be bioconductor/R, but as I am also using JMP13, i wondered if it is possible to transform my data into a box-cox or variance-stabilzing data format using JMP.
Many Thanks for your Help,
There is a nice sample data table that illustrates Box-Cox within JMP.
Help==>Sample Data Library
and then open the "Box-Cox" data table.
There is an embedded script in the data table called "Fit Model"
Run that script by clicking on the green trangle next to the script
In the displayed output, scroll down to the Box-Cox paragraph. The red triangle shows several actions you can take on the displayed transformation.
You can also use the "?" tool and click on the Box-Cox Transformations graph and get detailed help on the display.
And, just out of curiosity, why do you think "bioconductor/R" would be a better choice than JMP?