Problem in calculating the differential OTU abundance based on glm model ALDEx2 version 1.20.0

[mbaloza]

Hello,

I am trying to calculate the differential OTU abundance, I used this code

OTU_table=read.csv("PS118_physeq.csv", h=T)

OTU_St1_St4_2_3=OTU_table[,c(38,44,50,98,104,110)]

Remove rows having all zeros

OTU_St1_St4_2_3=OTU_St1_St4_2_3[rowSums(OTU_St1_St4_2_3[])>0,]

Conds<-c(rep("St4",3),rep("St1",3))

create an aldex object, which inludes clr transformation (so your input file is OTU_table with raw couts) and statistical test

St1St4_2_3=aldex(OTU_St1_St4_2_3, Conds, mc.samples=128, test="glm", effect=FALSE, include.sample.summary=FALSE, verbose=FALSE)

I got this error:

aldex.clr: generating Monte-Carlo instances and clr values
operating in serial mode
computing center with all features
aldex.glm: doing glm test based on a model matrix
Error in lr2glm(mci_lr, conditions, ...) :
Please define the aldex.clr object for a model.matrix 'conditions'.