Package PEER doesn't exist anymore

[sudha...@gmail.com]

Hi, we are trying to build the predictDB pipeline on custom gene expression data and need to generate PEER factors for the same but the package doesn't seem to exist anymore. Could you please guide us on alternatives?

Thanks,

Sudha

[Hae Kyung Im]

You can use principal components of the gene expression matrix instead. 

It’s been shown that PCs outperform PEER factors

Zhou, H.J., Li, L., Li, Y. et al. PCA outperforms popular hidden variable inference methods for molecular QTL mapping. Genome Biol 23, 210 (2022). https://doi.org/10.1186/s13059-022-02761-4

Zhou, H.J., Li, L., Li, Y. et al. PCA outperforms popular hidden variable inference methods for molecular QTL mapping. Genome Biol 23, 210 (2022). https://doi.org/10.1186/s13059-022-02761-4

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