How can I do this

Hi, I want to compare the community percentage composition between two groups.
For example, the data set like this.
site 1 site 2

Acidobacteria 30% 25%

Actinobacteria 24% 20%

Cyanobacteria 5% 6%
So on and so forth.

Site 1 and Site 2 can be two sites or the same site sampled in different seasons (e.g. spring, summer). I want to get some information if the community composition changed or not.

I was wondering which analysis/statistical methods can compare them directly.

The methods that i can think about is ANOVA?. Normally, if I use ANOVA, each site has to have multiple measurements (e.g., I have more than 2 sets of composition data in site 1 and site2)
Any command in mothur can do this? If not, can any one tell me which stats method can do this, I can do it in R.

Can fisher exact test or G-test do this? (I don’t think these two tests can use percentage data)


You can to this with metastats (command and paper).

You’ll need to create an appropriate shared file using phylotyping to get the phylum-level groupings, and then manually create your design file to attribute samples to site groupings, but the phylotyping is quite simple and design file just takes a few minutes in any text editor.

Hope that helps.

Thanks. Can you tell me attach or tell me where can I find your example design file

It’s just a two-column, tab-separated file with group names on the left, then treatments or metadata factors on the right. For example:

Group1 Summer
Group2 Summer
Group3 Summer
Group4 Winter
Group5 Winter
Group6 Winter