Can I use pseudocounts for differential abundance of OTUs?
Entering edit mode
dc • 0
Last seen 3.3 years ago

Hi community!!! This is my first post in this forum. I am working with WGS metagenome data profiled by MetaPhlAn software which gives relative abundance of OTUs (read count data of the OTUs is not provided). Now, I am doing statistical analysis with phyloseq package. I have converted my dataset from phyloseq to Deseq class. I want to find out which OTUs in my data sets are differentially expressed between control and test samples. So, my question and confusion is should I multiply the relative abundance data with some constant (e.g. 1 Million) converting the relative abundance to pseudo counts for Deseq analysis? Or, something else?

Many many thanks, from dc

metagenomics deseq2 PHYLOSEQ • 981 views
Entering edit mode
Last seen 5 hours ago
United States

I never recommend adding pseudocounts upstream of DESeq2 but don’t work in microbiome also.


Login before adding your answer.

Traffic: 519 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6