Hello, i am checking SVA for estimating batches in an expression atlas. This expression atlas is composed my multiple experiments (different dates) and multiple tissues analysed from wild type samples. Contrarily to the general aim of this analysis, i am not interested in performing a DE analysis, but i am interested in normalizing this data for a following a network analysis. For this reason i'll consider the two methods:
(1) SVA : identifying and estimating surrogate variables for unknown sources of variation. (2) ComBat: directly removing known batch effects using ComBat in SVA.
Potentially i have no adjustment variables nor variables of interest. For the 1st method what will be the full model matrix that i have to set?
Hope it is clear, Thanks in advance.