Cross-domain

[ntromas]

Hi,

I wonder if it would be possible to analyse cross domain interactions like with Spiec-easi? In that case, input would be 2 tables.

Thanks,

Nico

[lch14forever]

Hi Nico,

Unless the other input (than microbiome) also can be assumed to follow generalized Lotka-Volterra models. Otherwise, it might require to rewrite the model and derive the EM optimization.

Chenhao

[ntromas]

Hi, The other input is also a phyloseq object of the viral community. In total I have 2 phyloseq objects: one from the bacterial and another from the viral community. Le mar. 9 févr. 2021 19 h 20, Chenhao Li <[email protected]> a écrit :

…

Hi Nico, Unless the other input (than microbiome) also can be assumed to follow generalized Lotka-Volterra models. Otherwise, it might require to rewrite the model and derive the EM optimization. Chenhao — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6AMOGW2AF6D2LJUUW3S6HGL3ANCNFSM4XLRRXCQ> .

[lch14forever]

I think you could try using them as a single taxanomic matrix then.

[ntromas]

But the 2 objects come from different sequencing run/approach. Le mar. 9 févr. 2021 20 h 03, Chenhao Li <[email protected]> a écrit :

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I think you could try using them as a single taxanomic matrix then. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6BRD63WD5FEUMSYDWLS6HLN5ANCNFSM4XLRRXCQ> .

[lch14forever]

I see. I think it is a bit tricky because we will need the ratio of bacteria vs. virus in each sample...

[ntromas]

I don't have that...At best I have the relative abundance of each taxa for each table... Le mar. 9 févr. 2021 20 h 15, Chenhao Li <[email protected]> a écrit :

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I see. I think it is a bit tricky because we will need the ratio of bacteria vs. virus in each sample... — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6FD2OVWKHJY2YKULDTS6HM4TANCNFSM4XLRRXCQ> .