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lirongrossmann
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@lirongrossmann-13938
Last seen 3.9 years ago
Hello everyone,
I was wondering if there is a way to remove batch effect from an expression matrix (raw counts) for downstream analysis (like pca, clustering, machine learning) using the Deseq2 package.
I know I can do it using limma with removeBatchEffect, but wasn’t sure if there’s a similar function in Deseq2.
Thanks!
Thanks! Can I use the output for classification purposes as well or would you recommend a different strategies for accounting for confounders?
Depends on application. For statistical testing, we recommend to include confounder variables when possible as part of model as opposed to removing batch. But then for many possible tests, you could use DESeq() on counts. Otherwise, it seems easy to remove batch for e.g. visualization and prediction tasks.