Erro in peer.residual()

[Galaxy-228]

Hi,
I am testing based on the official documentation's test code, When running to this step: peer.exp <- peer.residual(mat, mat.aligner, covs, n.iteration=1000), the following error appeared:
Error in PEER_setCovariates(model, as.matrix(covs)) : SWIG:UnknownError

Do you know what caused the error?

Thanks so much

[lihaone]

It seems like an error from SWIG. Did you manage to install PEER and its dependencies properly?
Hao

[Galaxy-228]

Hi,
All the required R packages have been installed, Except for the version of the limma package.
When i type :

BiocManager::install('limma', version='3.8')
Error: Bioconductor version '3.8' requires R version '3.5'; use version = '3.16' with R version 4.2;

The current version of the limma package is 3.54.2.

packageDescription("limma")$Version
[1] "3.54.2"

In addition, may I ask if I can add you on WeChat for communication?

Best,
Jie

[lihaone]

I actually never saw this error before, but I think limma should not be the problem here.
I would suggest that you test the example code in the PEER tutorial (https://github.com/PMBio/peer/wiki/Tutorial), to see If the error remains.

[Galaxy-228]

Thanks so much for your reply,
I tested the test code according to your suggestions, and everything is running normally, and the peer version is 1.0.

Best,
Jie

[lihaone]

Can you try the PEER_setCovariates example code from the tutorial since it's the one that gave errors?