search

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/
587 stars 187 forks source link

Intra-individual comparison #776

Open nelly87 opened 7 years ago

nelly87 commented 7 years ago

Hi I have a phyloseq object with 100 samples (50 patients each with 2 samples), and sample data variables "sampleID" which is unique, "patientID" which is duplicated (because each patient was sampled at 2 sites, A & B) and "sample_site" variable which is either A or B.

I would like to carry out a within patient comparison (intra-individual) of their different sample collection sites. Specifically, each patient was sampled at two sites, A & B for instance, and I would like to check if the two sites differ within the same patient. Something similar to figure 2 of this paper: https://www.nature.com/articles/srep06602

Could you kindly advice me on the how (code wise) I can perform this analysis in phyloseq/other and to visualise the differences/similarities please? I don't mind a different visualisation plot from the one in the mentioned paper.

Thanks in advance, Nelly

pstevens2109 commented 3 years ago

Hi,

Have you found a way to resolve it ?

Thanks a lot !

Philippe