Adjusting for covariates (II)

Hello all –

I understand this has been asked, but would it make sense to run per-OTU linear models that include adjustment covariates (e.g., sex) and use the scaled residuals as input for SPLS(DA)? There are a few papers that have done something similar in the context of Spearman correlations, for instance.

Tanks very much.

hi @padimitriu,
Yes, you could, if there is no confounder between your covariate and the treatment effect. Otherwise some of the treatment effect will be lost before it will be input in sPLS-DA (or you may even generate new unwanted variation in the data). The correlation usually arises if the covariate-treatment design is unbalanced

Note: we are currently working on a method to remove batch effects, but only for one covariate: https://www.biorxiv.org/content/10.1101/2020.10.27.358283v1

Kim-Anh

Excelent – thank you for your reply.