I am analyzing the HumanMethylationEPIC array data. In order to remove batch effects and other unwanted variation, surrogate variable analysis (SVA) was conducted using the SmartSVA package. And then include the surrogate variables (SVs) as covariates in the linear model.
Question: If the sample size is small (for example, only 40), and there are many SVs (for example, 15). Do I need to adjust all SVs? If not, what criteria should I use to select the number of SVs?
I'm waiting for your help! Thanks!