Question: using technical replicates to batch correct
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gravatar for Juliet Hannah
3.4 years ago by
Juliet Hannah360
United States
Juliet Hannah360 wrote:

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 • 513 views
ADD COMMENTlink written 3.4 years ago by Juliet Hannah360

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

ADD REPLYlink written 3.4 years ago by chris86390

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.

ADD REPLYlink written 3.4 years ago by Juliet Hannah360

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

ADD REPLYlink written 3.4 years ago by chris86390
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