Entering edit mode
5.1 years ago
hansong798
▴
20
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?
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)?