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gabrielamaiz
Level I

Using Permanova in JMP

Hi,

I'm trying to run a PERMANOVA in JMP instead of Qiime to look at the differences in community composition among different microbial samples based on different factors. I'd also love to learn to build PCoa plots in JMP if possible, but this is secondary.

Thank you!

7 REPLIES 7
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ian_jmp
Staff

Re: Using Permanova in JMP

There's nothing built in to JMP directly comparable to http://qiime.org/scripts/compare_categories.html (not in detail at least).But if you are able to give some more details of the variables you have, I'm sure folks will have some suggestions as to how you may proceed using JMP capabilities. Various 'extra' things may be feasible by using JMP's scripting language, but I would not start with that.

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gabrielamaiz
Level I

Re: Using Permanova in JMP

Thank you Ian,


I'm attempting to run a PERMANOVA in JMP instead of Qiime to look at the differences in community composition among different microbial samples based on different factors. Most of the factors I would like to test are nominal and ordinal variables. 

Ex- Do breast-fed infant microbiomes differ in community composition from formula-fed infants at different ages?

The feeding variable has three nominal categories “Breast,” “Formula” and “Mixture,” and the age group variable has four levels  (0-3 mo., 4-7 mo, 8-11 mo or 12+ mo). Specifically I'd like to test if breast fed infants (0-3mo) differ from formula fed infants of the same age group, and so on.

Another variable is an ordinal scale of household cleanliness 0-2. 

   

I would also like to test the analysis of similarity (ANOSIM) if possible.

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marxx
Level III

Re: Using Permanova in JMP

Two years later. No responses?

 

PERMANOVA and ANOSIM are workhorses of the microbiome field. They need to be in JMP.

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Re: Using Permanova in JMP

These two methods have not yet been implemented in JMP. Please add them to the Wish List so others can vote (Kudo) on them. This will help the developers prioritize features for the next version.

 

Here is the link to the wish list:

https://community.jmp.com/t5/JMP-Wish-List/idb-p/jmp-wish-list

 

I agree it would be good to get these two on this list.

 

Best,

 

Chris Kirchberg

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com
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marxx
Level III

Re: Using Permanova in JMP

Thank you Chris, I have done so now and hope that it gets traction.

 

Much appreciated, marxx

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abmayfield
Level V

Re: Using Permanova in JMP

As someone who has to run a parallel operating system solely to run PRIMER (PC-only) to carryout PERMANOVA and ANOSIM, I strongly recommend that this technique be implemented in future JMP releases! I feel like all the major elements are in place already to make this happen. 

Anderson B. Mayfield
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Re: Using Permanova in JMP

Anyone stumbling onto this discussion may want to consider voting up the item in the wish list: PERMANOVA and PERMDISP 

Thanks, 

-John

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