Hello, I want to normalise my microbiome data (OTU table) using edgeR package and export my normalised matrix ( I want to test some normalisation methods, normalised data will serve to calculate beta diversity and visualise by PCoA). I went through bioconductor forum and biostars and I still don't know want is the proper way to export normalised data from edgeR.

So, I read my matrix and calcNorm:

d <- DGEList(counts = d, group=group)
d = calcNormFactors(d)

what happens next?:

1st option

d = estimateCommonDisp(d, verbose=TRUE)
normalised_df <- d$pseudo.alt

2nd option

normalised_df <- cpm(d,  normalized.lib.sizes = T)

3rd option

dgList <- estimateCommonDisp(dgList)
dgList <- estimateTagwiseDisp(dgList)
normalised_df <- t(t(dgList$pseudo.counts)*(dgList$samples$norm.factors))

I have an impression that every post claims something different and at this point I am very confused. Thank you!