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Published 20 hours ago • verified publisher icon KrishnaswamyLab

Using MAGIC with a combined dataset

Open saeedfc opened this issue 4 years ago • 4 comments

Hi,

I have to combine several datasets. Batch correction is used for clustering and Dimensionality reduction. But for visualization and DEG analysis I will be using normalized RNA counts (Seurat NormalizeData() function). Hence I have two options to get an imputed matrix for gene expression visulaization or DEG analysis.

  1. Do magic imputation on individual datasets and combine the matrices.
  2. Impute the combined matrix with magic.

What would be best? Or it doesn't make any difference? Any Help is appreciated, Kind regards, Saeed

saeedfc avatar Feb 07 '21 21:02 saeedfc

Hello, I am facing the same problem, do you have an exact answer now?

Emma1997WTT avatar Jul 10 '22 07:07 Emma1997WTT