ValueError: operands could not be broadcast together with shapes (17,) (16,32) about mambo HOT 8 OPEN

Hi,
You should have a numpy array with 17 numbers corresponding to the relative abundance o each of your 17 species. If your print the shape, it should return (17,). I am not sure what you have that is shaped (16, 32).

Best,
Daniel

from mambo.

Thank you for your answer.I made adjustments, and now the result is like this：

“ValueError: operands could not be broadcast together with shapes (17,) (17,32) ”

Each of my model has a set of abundance data at different sample points.

from mambo.

Sorry, you need to run them one by one :(

You can always write a script that runs each sample in parallel.

from mambo.

Thank you very much for your reply！
Best,
ming

from mambo.

from mambo.

Hi Yiming,

You are correct, but probably the other way around. The negative fluxes in the exchange reactions are consumed while the positive are secreted (unless there is some transformation going on. For instance, multiplying the flux by "-1")

If you have further questions, feel free to ask and I will answer as soon as I can.

Best,
Daniel

from mambo.

from mambo.

Hi Yiming,

The output is a Markov chain that contains a distribution of metabolite abundances and correlation to your metagenomics profiles.

Like in this Fig:

You should pullout the ones with a high correlation, together they are samples from a distribution rather than a single value.

Depending on your application, you can use the average or take the median of this distribution as your metabolome. As an indirect measure of "convergence" you can check that when you use this metabolome as your media, the relative biomass fluxes are highly correlated to the metagenome abundance profile.

Hope this helps. Feel free to email me if have some specific questions or want to discuss your data in person: [email protected]

Best,
Daniel

from mambo.