Hi all,
I wanted to know if the ‘normalization’ and ‘transform’ parameters of MTXmodel package were applied on both mtx and mgx data ? Or should I normalise and transform the input dna data prior running the package ?
Thank you
Hi all,
I wanted to know if the ‘normalization’ and ‘transform’ parameters of MTXmodel package were applied on both mtx and mgx data ? Or should I normalise and transform the input dna data prior running the package ?
Thank you
Hi,
The MTXmodel package will normalize and transform both (code here). However, I’d recommend using MaAsLin 3 for this since it has an explicit function preprocess_dna_mtx
to pre-normalize and transform the DNA in addition to handling scenarios in which one or both of the DNA/RNA values are 0. An explanation of how to use this is available in the tutorial.