Question: Can I use pseudocounts for differential abundance of OTUs?
gravatar for dpc
12 weeks ago by
dpc150 wrote:

Hi !!! I am working with WGS metagenome data profiled by MetaPhlAn software which gives relative abundance of taxa (no read count data of the taxa is provided). Now, I want to find out which are the significantly differentially present taxa between the test and the control samples with DESEQ package. So, my question 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? Will it give correct result?

Thanks, dpc

deseq • 196 views
ADD COMMENTlink modified 12 weeks ago by antonioggsousa1.5k • written 12 weeks ago by dpc150
gravatar for antonioggsousa
12 weeks ago by
antonioggsousa1.5k wrote:


I don't think that you can do it, because DESeq2 uses raw counts or estimated counts:

This post might help: A: DESeq2 of log2(count+1) transformed TCGA htseq counts from Xenabrowser


ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by antonioggsousa1.5k

Do you have any idea how can I find out (statistically) the differentially abundant taxa from metaphlan output?

ADD REPLYlink written 4 weeks ago by dpc150


I never use it myself, but LEFSe seems to do what you're interested in. It uses relative abundances to find differential abundant features (OTUs/taxa/genes) ranked by effect size:

Actually this method was developed by the same lab that developed metaphlan, so I think they are compatible, but as I said I never used them, therefore I can't be sure.

I hope this helps,


ADD REPLYlink written 29 days ago by antonioggsousa1.5k

Thanks, Antonio. Yes, I have already used it. I asked just to have a cross-check my data with another method if available.

ADD REPLYlink written 29 days ago by dpc150
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