Can I use pseudocounts for differential abundance of OTUs?
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dc • 0
@dc-23922
Last seen 13 months 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 • 256 views
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@mikelove
Last seen 8 hours ago
United States

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

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