formula <- ~DIAGNOSIS
refs <- 'CD'
refs <- 'Not IBD'
dat <- prepare_data(otu_table=GEVERS$OTU,rows_are_taxa=FALSE,tax_table=GEVERS$TAX,
metadata=GEVERS$META,formula=formula,refs=refs,
cn_normalize=TRUE,drop=TRUE)
the results are same. refs did not work, there is something wrong in this function.
formula <- ~DIAGNOSIS refs <- 'CD' refs <- 'Not IBD' dat <- prepare_data(otu_table=GEVERS$OTU,rows_are_taxa=FALSE,tax_table=GEVERS$TAX, metadata=GEVERS$META,formula=formula,refs=refs, cn_normalize=TRUE,drop=TRUE) the results are same. refs did not work, there is something wrong in this function.