I am having problems with the Aldex2 effect function. Can anyone help me please?


Aldex() works fine, I think. I used a t test for pre and post treatment. I have all the data from rab.all and ending with wi.eBH. I saw the manual says to run effect first before plotting. Like I mentioned, I have a pre and post data -- and 4 replicates each. When I run my clr data as x in aldex.effect() I first get an error:

x.effect <- aldex.effect(x, verbose=TRUE, include.sample.summary=FALSE, useMC=FALSE, CI=FALSE, glm.conds=NULL)

no applicable method for @ applied to an object of class "data.frame"

So, I tried to pull my data into an S4 using:
MyMatrix<-setClass("MyMatrix",slots = list(conds = "matrix"))

my_matrix_instance <- MyMatrix(conds = x)

x.effect <- aldex.effect(my_matrix_instance, verbose=TRUE, include.sample.summary=FALSE, useMC=FALSE, CI=FALSE, glm.conds=NULL)

Now I get an error, please provide a binary condition vector.

I am wondering what else I can try? Or is there something that I missed?

Thank you.

Hi @stacy,
I will leave this post queued for a bit in case any other mods have an idea of whats going on.

However, you might get a better reponse if you post an issue on the aldex2 github, it seems like its still being actively maintained: GitHub - ggloor/ALDEx_bioc: ALDEx_bioc is the working directory for updating bioconductor