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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Rarefy and Restroom example #1595

Open mweberr opened 2 years ago

mweberr commented 2 years ago

Hi all,

I found several opinions about the rarefy_even_depth procedure and also in the manual it is stated that the procedure is not advocated. I am a beginner in microbiome analysis and I started with the restroom example, which is a really good start to using phyloseq. http://joey711.github.io/phyloseq-demo/Restroom-Biogeography

In the example rarefy_even_depth is set to 500 to reproduce the results in a paper. However, this was compiled in 2013. I am wondering what would be the recommended approach in 2022 to show barplots of the most abundant families ? Would you still rarefy to a very small common number of reads (500) or directly transform each sample, even total read number differs largely (up to 10k) ?

Best, Michael

benjjneb commented 2 years ago

For creating barplots of proportions, I would probably just transform the data to proportions without an intermediate rarefying step. The proportion transformation takes care of the sampling size differences there. Rarefying might be needed for other types of analysis, e.g. richness estimates.