compare_alpha_diversity.py

[Luz Chacón Jiménez]

Hi!

I want to use this script to compare 3 different treatment for my samples. 

The Description of the script only inform that is a T test. But, what kind of T test is? For different samples?, for related samples? Can I modiffy the type of t test? 

Thanks,

[Justine Debelius]

Hello Luz,

I find the html documentation really helpful when I'm trying to understand scripts: http://qiime.org/scripts/compare_alpha_diversity.html. They're sometimes a little bit easier to read than the command line. You will find the answer to your first two questions in the example description near the bottom. You cannot modify the type of test.

Best,

Justine

[Hiunvun Chin]

Hi,
I have the same question. How about if i have more than 2 groups to compare? Since t-test is comparing the means of 2 groups. If 3 groups and above, we need to do ANOVA. I wonder Qiime can do this?
Thanks!
Chin

[Justine Debelius]

As I read the documentation, compare_alpha_diversity will do pairwise comparisons between each set of two groups. So, if you have groups A, B, and C, you'll get A vs B, A vs C and B vs C.

Best,

Justine