adonis and anosim

[yings...@126.com]

 when i run compare_categories.py, using method adonis or anosim,  some results is that the p-value > 0.05 and the R is close to 0. what's that meaning? is it mean that the there are no significant differences between those groups?

[Greg Caporaso]

Yes, that is correct. 

Greg

[Becky]

I am evaluating my anoism and adnois values I want to double check that I am understanding what is written under qiime/scripts for both measures. So based on the previous post p-values of 0-0.04 = significant differences and p-values of 0.05 and greater = no significant differences?

[Kyle Bittinger]

Yes, that is correct.

On Tue, Sep 24, 2013 at 4:46 PM, Becky <rmul...@gmail.com> wrote:

I am evaluating my anoism and adnois values I want to double check that I am understanding what is written under qiime/scripts for both measures. So based on the previous post p-values of 0-0.04 = significant differences and p-values of 0.05 and greater = no significant differences?

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[Greg Caporaso]

This is actually something that the user needs to think about, rather
than there being a hard cut-off for statistical significance. An alpha
of 0.05 (i.e., less than 0.05 is considered significant) is common,
but the choice of alpha is something that you need to decide based on
whether you'd rather have false positives or false negatives.

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[mohsen pourabedin]

I used ANOSIM and  R is 0.26, p value=0.001.  To me, the p value shows significant difference but having low correlation coefficient make it difficult to conclude.

How you guys interpret it.

Thanks

Mohsen

[Ivy Yang]

Hi Greg, 

My annosim result in on the other extreme. I have DNA extracted from two groups of samples, one group (3 samples) was extracted from large sludge, and the other (another 3 samples) was from small sludge. When I set large vs. small as the category, I got p-value = 0.12 with R=1 with 999 permutation. 

Does that mean the two groups might be different, but the difference is not statistically significant? 

Thanks. 

Ivy

[Jai Ram Rideout]

Hi Ivy,

That depends on what alpha you chose when performing the test. If you chose an alpha of 0.05, then yes, your interpretation sounds correct to me.

-Jai

[Guan Wei Kang]

Hi,

base on my workflow, it seems the output for my compare_categories.py command seems to be reflective of my results from beta_diversity_through_plots.py command. i would be grateful if someone can shed light on the meaning behind the p-value as well as the r statistic or point me in the right direction for any external reading sources.

thanks for the assistance.

rgds,

guan

[Jai Ram Rideout]

Hi Guan,

Run the script in help mode for some basic info about the methods -- the help text also describes where to find more details about these methods.

compare_categories.py -h

-Jai

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