Hi everyone, I have a small question. I have two samples data. Each sample contains around 55 cloned sequences. I use Mothur solfware to calculate Shannon index of 2 samples. Which hypothesis test I should use to decide whether two values (97% similarity) are significantly different or not? For each sample, I receive the result of shannon index at different similarities with corresponding lower confidence interval and high confidence interval.
See if this may help
http://www.loujost.com/Statistics%20and%20Physics/Diversity%20and%20Similarity/How%20to%20compare%20the%20diversities%20of%20two%20communities.htm
Hey, can you provide the Mothur results? which mothur command did you use? If you just wanna verify the significant difference between two shannon index, you have to do it in the way that Jason said because two samples are way too small to perform T-test. If you just wanna know if two community structures are truely different or not, you can try Unifrac analysis but still, if you just have two samples, there's no need to perform any statistical analysis.
Hi every one, I have find information from Subhash Chandra's sugession with key words-Comparing the diversities of two communities. They use t test for decide whether there is significant difference between two communities. I wonder can I use the t test for Shannon index. I attach the reference at attach file.
Hi Jason Neil Waite: attually, I have not yet understood your method you use due to my week background in statistic.
Hi Fang Liu: I use command summary.single (calc=Shannon) in Mothur solfware.
Hi Jason Neil Waite,
I have not yet try to use R, but I would like to receive your example code and practice.
Thank you very much for your explanation in detail.
Thank you very much for your information, Jason Neil Waite.
Best regards,
Pham Ngoc Dung
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