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Are there tools implemented in Bioconductor that allow one to use technical replicates to batch correct. Meaning, if one has a group of samples that are repeated across known batches, are there tools that can use these samples for batch correction?
I am pretty sure you just need to read about the SVA package manual, I use combat and then PVCA to assess correction. https://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf
Thanks for your input. To clarify, I am not trying to use the samples to assess the success of batch correction. I am wondering if I can use the fact that they should be the same to model the batch correction. Thanks again.
If you mean model and correct the data yeah you can, you can just use COMBAT.... Excuse me if I am misunderstanding your question.