Can you please help me verify my NMDS result from MaAslin output ?

#1

Hello Dear Galaxy team

My name is Hadar Mor and I am a Ph.D student at Omry Koren Lab at the Bar-Ilan University in Israel.

Can you please see the attached NMDS fig that was done by MaAslin on the Galaxy website.

The general concept of our project- We treated mice with Lupus nephropathy with TPC vs. PBS (control) and saw significant improvement in the protein levels in the urine, in the kidneys histology and also in the pro-inflammatory cytokines levels.

My question is- whether this fig illustrate the fact that TPC is improving proteinuria (high levels of protein in the urine)?

It is a fig that we want to add to our paper results that we are returning back now after minor revision. We will appreciate if you can please have a quick look and give us an answer quickly because we intend to send the article back today, just before Christmas vacation.

Thanks a lot in advance!

Hadar

#2

Hi - The graphic was not attached. Would you please post it if you still want want feedback?

#3

Hi Jenna I will be happy to get any feedback from you.
here is the output file I got.

Is there is way that I can get the row data of my NMDS analysis (for each sample) wich was done by MaAslin on the Galaxy website. Becouse I want to calculate the distances and the angles of the three vectors and get some significancy to this beautiful result!
Additionly how can I know the group belonging of each dot on the graph?

Hope you can see the attached png file.
Thanks a lot!
Hadar

image
image.png623×618 16.4 KB

#4

This is the Galaxy server you are working at? http://huttenhower.org/galaxy

It looks as if the Galaxy wrapped version of the tool is still undergoing some development and hasn’t been published to the ToolShed yet. Re: http://huttenhower.sph.harvard.edu/maaslin

I would suggest contacting either the tool author ttickle@hsph.harvard.edu or using the tool’s Google group https://groups.google.com/forum/#!forum/maaslin-users for help with the functions – some appear to be included so far and some are not. These are the experts that can help to ensure that the inputs are set up correctly for the functions that are implemented.

Note: There is a much older version in the ToolShed https://usegalaxy.org/toolshed that should probably be avoided. I don’t know how the two versions compare in terms of functionality but that repository hasn’t been updated since 2015 and may not install well into Galaxy anymore.