Can I use baseMean (from DESeq2) as part of presenting/ interpreting results
1
0
Entering edit mode
@a20bc3af
Last seen 11 months ago
United Kingdom

Hi,

This is my first time posting here. I have sequenced 16s rRNA from faecal samples. I am looking at differential abundance analysis (DAA) using DESeq2. I wanted to know if there are significant DAA between older and younger aged people. I got over 80 OTU sequences as being significantly DAA (P<0.05). Can I use baseMean to select out OTU which are most prevalent/ abundant? I.e. can I use the top five highest baseMeans to identify which OTUs are most abundant?

DESeq2 diferentialabundance 16srRNA baseMean • 396 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 hour ago
United States

The microbiome community may have different methods which are more appropriate to analyze 16S data. I'm not an expert in the best methods used now. It seems like the mean of scaled counts is a reasonable measure of abundance, but you'd need the scaling to be appropriate to the data type. Median ratio is appropriate for most bulk RNA-seq but it has been argued that microbiome requires alternative approaches.

ADD COMMENT

Login before adding your answer.

Traffic: 917 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