FAMT Agrocampus ouest

How do I install the FAMT package?

Open a R session, download the package
and write: library(FAMT)

I don't have the 'Annotations' dataset. Can I use the package?

Yes, you can. The Annotations dataset is optional to create a FAMTdata (see asFAMTdata function).

I want to use the package without applying the FA method.

You can use the package without applying the FA method.
The modelFAMT function performs classical multiple testing statistics when you put the argument 'nbf' equal to 0 (see Tutorial).

I can't create the FAMTdata?

The as.FAMTdata function checks the consistency between Expression and Covariates. If there is no consistency, the FAMTdata is not created. The covariates dataset needs a column containing the array identification to match Expression and Covariates. This identification column must be defined with the argument 'idcovar'. The figure below shows the FAMTdata:

What about missing values?

The as.FAMTdata function allows to impute missing values (we use the impute.knn function of the impute package). If you want to apply another method to impute missing values, select na.action=FALSE in the as.FAMTdata function (see Tutorial). However there must be no missing expression data to create a FAMTdata.