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?

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.