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ggloor / ALDEx2_dev

ALDEx tool to examine compositional high-throughput sequence data with Welch's t-test
GNU Affero General Public License v3.0
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Problem in calculating the differential OTU abundance based on glm model ALDEx2 version 1.20.0 #27

Open mbaloza opened 2 years ago

mbaloza commented 2 years ago

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'.