Question: Can I use pseudocounts for differential abundance of OTUs?
1
gravatar for dpc
12 weeks ago by
dpc150
India
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
0
gravatar for antonioggsousa
12 weeks ago by
antonioggsousa1.5k
antonioggsousa1.5k wrote:

Hi,

I don't think that you can do it, because DESeq2 uses raw counts or estimated counts: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#input-data

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

António

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
2

Hi,

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: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-6-r60

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,

António

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1760 users visited in the last hour