export ANCOM-BC normalisation matrix
0
0
Entering edit mode
11 weeks ago
fyfes ▴ 30

Hello, I want to normalise my microbiome data (otu table) using ancom-bc (I want to have a csv file with data that is normalised for library size). I am doing that:

feature.table=feature_table; sample.var="sample_id"; group.var="group" zero.cut=0.90; lib.cut=1000; neg.lb=FALSE pre.process=feature_table_pre_process(feature.table, metdadata, sample.var, 
                                      group.var, zero.cut, lib.cut, neg.lb)

feature.table=pre.process$feature.table

Am I doing it right? is my feature.table my normalised matrix? I am asking as after feature_table_pre_process I have the same values but some of my OTUs are gone.

microbiome normalisation • 140 views
ADD COMMENT

Login before adding your answer.

Traffic: 2274 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6