We know packages like SVA and ComBat, which can be used to adjust data for batch effects or biological artifacts. However, in most cases, all adjusting variables are treated as factors. So I want to know whether anyone could suggest me any package where in I could adjust for the "continuous" variables/covariates. I have multiple of them to adjust for. Could anyone suggest me an easy-to-use method?

I have also read about "cbcbSEQ" with a modified ComBat function (Post: How To Adjust Data For Confounding Covariates Before Pca?). Has anyone tried it for continuous variables?

In R you can just include the values of the continuous variable in your design matrix

@russ_hyde.. thanks for your reply. But I do not quite understand how do I do that. I do not want to include these covariates in my linear model. I would like to adjust for them separately in my data and then work with the adjusted residual matrix.