using technical replicates to batch correct
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Juliet Hannah ▴ 360
@juliet-hannah-4531
Last seen 4.9 years ago
United States

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?

batch effect • 1.0k views
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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

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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.

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If you mean model and correct the data yeah you can, you can just use COMBAT.... Excuse me if I am misunderstanding your question.

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