RUVg using positive control genes (ERCC mix 1 & mix 2)

[mariana19901990]

Hi,

I am using RUVg to analyze RNA-seq data from 12 samples. Six of those samples are control and have ERCC mix 1, while the other six samples are treatment samples and have the ERCC mix 2. Therefore I have positive and negative controls. In the RUVseq paper and the vignette is specified that is possible to use the positive and the negative controls by centering them (logY- X B) and running RUVg on the centered controls. However I don't understand how center the controls. How to build X? Which is the intercept in X? is B the expected fold change?

Thanks