Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
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Last seen 15 months ago

Hello everyone, First, I am so sorry if my post title does not correspond to my post completely.

I am using scater/scran package for scRNA-Seq analysis and MNN for batch correction.

As I know with multiple datasets; MNN integrates first and second datasets first and integrate the third one with first-and-second-integrated data set. After the analysis, I have a MNN-corrected space.

I want to do something like this if possible: Let's say I have 3 different scRNA-Seq (first experiment set) data and will have 2 more (second experiment set) in a month. I used MNN for the first experiment set and have an MNN-corrected values. Is it possible to keep that values and integrate the new data sets to that corrected values. I want to have the MNN corrected values of first experiment after integration with second experiment set. Corrected values of first experiment have to be same and second experiment will be integrated to the corrected space.

Or; is there a way to do batch correction on cell basis, like a scaling factor that integrates all cell to the same space?

I am really sorry about my post. I was little hard to explain without drawing on a paper.

Thank you in advance.

scater singlecell scran BatchEffect • 641 views

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