Covariate remove from Expressionset using SVA to yield transformed_expressionset

Question

[brianscomer]

This may be a naive question but I am fairly new to bioinformatics and R in general.

I need to perform eQTL analysis using GGtools and I am attempting to make a smlSet (genotype matrix + expressionset) using functions in GGtools. Is there a way I can correct my expressionset using SVA to generate a transformed expressionset directly as opposed to the typical workflow which uses the matrix output from SVA to perform linear regressions via limma() or a similar function.

Sorry if this seems simple but perhaps I am simply missing something simple.

Answer 1

[brianscomer]

Actually, I found the answer to my question in another post:

Remove Surrogate Variables and Batch