How can I do this

Commands in mothur
1

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)

Thanks,

2

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.

3

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

design=temp.job2.design

4

http://www.mothur.org/wiki/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