How to perform batch correction on scRNA-seq with confounding plate effects?
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jashmore • 0
@jashmore-23116
Last seen 10 weeks ago
United Kingdom

I have scRNA-seq data generated by Smart-seq2 which includes one plate of wild-type cells and a separate plate of knock-out cells. I would like to combine the data from these two plates in order to investigate any effects caused by the experimental intervention. I understand that plate and genotype are confounded in this design, but can fastMNN still be used to integrate such data? My approach would be to analyse the plates separately then merge them with fastMNN and re-do the dimensionality reduction and clustering so I can perform some comparative analyses. Are there any caveats or limitations to this approach that I should keep in mind?

batchelor • 144 views
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Aaron Lun ★ 27k
@alun
Last seen 3 hours ago
The city by the bay

I understand that plate and genotype are confounded in this design, but can fastMNN still be used to integrate such data?

Yes, that's fine, but read this.

My approach would be to analyse the plates separately then merge them with fastMNN and re-do the dimensionality reduction and clustering so I can perform some comparative analyses. Are there any caveats or limitations to this approach that I should keep in mind?

That is also fine, and in fact a comparison of the separate and combined analyses is the basis of one of our suggested diagnostics here.

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