Using DADA2 output for DESeq2
1
0
Entering edit mode
@blastzoneheimerdinger-15116
Last seen 3.0 years ago

Hello, sir.

I have a question regarding using microbiome dataset for DESeq2. I used DADA2 and got like 200 samples X 3000 RSVs table. I want to determine which RSV are differentially abundant across groups.

My question is that should we feed raw 3000 RSVsĀ  to DESeq2, or should we feed agglomerated RSVs (like 100~ genera by phyloseq function tax_glom()) to DESeq2? I read the vignette and find that we are to feed raw count data to DESeq2, but I have many output that differentially abundant across groups which share same genera.

Thanks in advance for help.

deseq2 dada2 • 1.2k views
ADD COMMENT
1
Entering edit mode

I don't myself analyze microbiome data, so I'll leave this one to the experts.

ADD REPLY
0
Entering edit mode

Thank you very much for reply, and developing this wonderful package.

ADD REPLY
3
Entering edit mode
@benjaminjcallahan-9771
Last seen 17 months ago

Performing differential abundance testing is valid at the ASV level, or at the genus level. The optimal choice really depends on your scientific question, and the phylogenetic depth at which the phenotypic traits relevant to that question are conserved.

This is anecdotal, but when I am doing differential abundance testing in microbiome data, I usually (1) perform independent filtering and remove low prevalence ASVs to reduce the multiple testing burden, (2) test at the ASV level, (3) test at the genus (or somtimes higher) level. So, "and" instead of "or".

ADD COMMENT
0
Entering edit mode

Thank you very much for the reply and clarity. This really answers my question. I will try first to do ASV-level testing. How great this forum is, to immediately got answers from actual developer of DADA2 and DESeq2!

ADD REPLY

Login before adding your answer.

Traffic: 528 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