How to remove batch effects using surrogate variables?

Question

[hansong798]

My methylation data has about 800 sample and 300,000 variables and I found 26 surrogate variables using 'DoISVA' package in r.

The problem is that r function that remove batch effects like 'removeBatchEffect' or 'ComBat' can get only 1 or 2 batch effect as input. However, in mycase, I want to remove batch effect using 26 surrogate variables.

Is there suitable any r package or other possible way to solve this problem?

[Kevin Blighe]

26?! ...do you want to eliminate every last bit of useful information from your data? Why do you feel the need to remove batch effects? - is there genuinely a batch effect (have you checked)?