Box-Cox or VST transformation of RNAseq Data

Question

Dear community,

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,

Markus

MarkusEckstein · Answer

Many Thanks. Do you know how to apply this Script on my data ? What are the other variables in my RNAseq setting ?

Chris_Kirchberg · Answer

In JMP Genomics you can normalize the data using TPM, RPM, KDMM, TMM and Upper Quartile.

Various transformations can be done such as log square root, etc.

JMP Genomics is probably better suited for very tall data sets like you might have as transcripts/genes are rows and samples are columns.

https://www.jmp.com/en_us/software/jmp-genomics.html

Chris

txnelson · Answer

There is a nice sample data table that illustrates Box-Cox within JMP.

Go to:

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?