Covariate remove from Expressionset using SVA to yield transformed_expressionset
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.
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brianscomer •
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Actually, I found the answer to my question in another post:
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