Comparison of confound adjustment methods in the construction of gene co-expression networks

Cote, A. C.; Young, H. E.; Huckins, L. M.

doi:10.1101/2021.05.18.444709

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bioRxiv · 10.1101/2021.05.18.444709

Comparison of confound adjustment methods in the construction of gene co-expression networks

Cote, A. C.·Young, H. E.·Huckins, L. M.

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Abstract

Adjustment for confounding sources of expression variation is an important preprocessing step in large gene expression studies, but the effect of confound adjustment on co-expression network analysis has not been well-characterized. Here, we demonstrate that the choice of confound adjustment method can have a considerable effect on the architecture of the resulting co-expression network. We compare standard and alternative confound adjustment methods and provide recommendations for their use in the construction of gene co-expression networks from bulk tissue RNA-seq datasets.

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Cote, A. C., Young, H. E., Huckins, L. M.. 2021-05-20. Comparison of confound adjustment methods in the construction of gene co-expression networks. https://doi.org/10.1101/2021.05.18.444709

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