**20**wrote:

This question is split into 2 parts:

(1) **Can TMM normalization through edgeR be used for other count data like OTU counts and contig counts? **

(2) A**fter you calculate TMM, would converting to RPKM be more useful for looking at contig counts data since the range of lengths is pretty wide;** if the above is a Yes: (pseudo-ish code below)

scalefactors = (normfactors * libsize)/1e6 df_tmm = df_counts / scalefactors # In Python # scale(df_counts, center=FALSE, scale=(normfactors * libsize / 1e6)) # In R df_tmm_rpkm = (df_tmm / seq_lengths)*1000

**52k**• written 2.6 years ago by jol.espinoz •

**20**