Question: Covariate remove from Expressionset using SVA to yield transformed_expressionset
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gravatar for brianscomer
4.8 years ago by
brianscomer0 wrote:

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.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by brianscomer0
1
gravatar for brianscomer
4.8 years ago by
brianscomer0 wrote:

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

Remove Surrogate Variables and Batch

ADD COMMENTlink written 4.8 years ago by brianscomer0
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