Question: Algorithm to remove batch effects
gravatar for fouerghi20
15 days ago by
fouerghi2030 wrote:

From your own experience, is it better to do batch effect correction with Seurat (using CCA) or through Harmony (using it through the Seurat Wrappers)?

ADD COMMENTlink written 15 days ago by fouerghi2030

Neither, I had best results with fastMNN from the Bioconductor package batchelor. Depends on the magnitude of the batch effect though. Sometimes, if it is only some minor technical variation, like the basically same material prepared on two different days maybe even something simple as regression on the logcounts can be enough. On the other hand if the actual difference that you aim to remove is a pertubation effect that confounds the clustering then more stringent methods are required. You would need some details about your samples. What are they, are the same celltypes expected in both batches, is there a pertubation involved...

As usual in this context I will recommend to read the relevant paragraph in our holy single-cell bible OSCA:

ADD REPLYlink modified 14 days ago • written 15 days ago by ATpoint44k

You may also find this previous discussion helpful: about batch correction in scRNA-seq

ADD REPLYlink written 14 days ago by igor12k
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