Cross-domain analysis with virus and bacteria abundance matrices

[07Chengran]

Hi,

I'm working on a cross-domain analysis using a virus-relative abundance matrix and a bacteria abundance matrix obtained by metagenomic sequencing. When I ran the following script, I encountered a warning:

spiec.gl.out = spiec.easi(
    list(otus.f.bac, otus.vir),
    method = "glasso",
    icov.select.params = list(rep.num = 20),
    lambda.min.ratio = 0.01,
    nlambda = 100,
    pulsar.params = list(thresh = 0.15)
)

The warning message was:

Applying data transformations...
Selecting a model with pulsar using stars...
Fitting final estimate with glasso...
done
Warning message:
In spiec.easi.list(list(otus.f.bac, otus.vir), method = "glasso",  :
  input list contains data of mixed classes.

Despite the warning, the output was generated, and the network seemed fine. However, I'm curious about the meaning of the message 'input list contains data of mixed classes.' Does this warning have any implications for the accuracy or reliability of the network construction? How can I resolve this issue?

Additionally, when I set thresh to 0.1 or 0.05, I always receive the warning: "Optimal lambda may be larger than the supplied," regardless of whether I adjust lambda.min.ratio to 1e-2 or 0.1. Would it be acceptable to set thresh to 0.15, or could this impact the validity of the results?

Thank you for your help!