test_differential_abundance with batch effect

[MEladawi]

I wanted to inquire if there is a way to account for covariates effects using test_differential_abundance? Also, is there a way to support MaAsLin2 in the MicrobiotaProcess pipeline without manually extracting abundance then adding the differential analysis results?

Thanks!

[xiangpin]

I wanted to inquire if there is a way to account for covariates effects using test_differential_abundance?

• Maybe you can refer to the vignette of test_differential_abundance in tidybulk. I think you can use .formula to design your model.

is there a way to support MaAsLin2 in the MicrobiotaProcess pipeline without manually extracting abundance then adding the differential analysis results?

• MaAsLin2 has many dependencies, it is not a good idea to link the MPSE object by depending on it directly. Since it is too bad to maintain the package. Maybe we need to develop some scripts (not put them in MicrobiotaProcess package) to help to perform these.

[MEladawi]

Thank you. I am sorry I meant mp_diff_analysis, is there a way to use a formula in it?

re: MaAsLin2, it makes sense.

Thanks.

[xiangpin]

The current version didn't support the multiple covariates. We only consider the group or contained subgroup (eg: subgroup of some patients). We will account for the covariate effect in the next version.