Maaslin2: Normalisation and Transformation

[Jordan]

Hi All, 

I just want to know if I understand which function to do. 

If using compositional data (relative abundance) in Maaslin2... do we need still need to normalize using CSS/ TSS OR just transform (LOG or AST) the data....?

OR is it best to use count data then apply CSS AND LOG transformation?

Many thanks in advance, 

J

[Kelsey Thompson]

Hi Jordan,

The great part of MaAsLin2 is that you can either feed it raw count data and the default is that it will do TSS normalization for you or you can feed it normalized data and within the code put normalization = "NONE". The same goes for transforming the data the default is a LOG transformation, however you can also turn that off if you have already transformed the feature table before you run the model. 

I hope that helps! 

Kelsey