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andygxzeng / BoneMarrowMap

A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations
GNU General Public License v3.0
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Using cca integration instead of harmony #7

Open 2019surbhi opened 3 months ago

2019surbhi commented 3 months ago

Can you provide gene expression matrix for this dataset or add an option to perform batch correction using Seurat's integrated.ccca method instead of Harmony? I process my dataset using integrated.cca batch correction.

It makes sense that the ref and query needs to be processed the same way but when I project back the prediction to my UMAP, the predictions don't fit my UMAP structure and clustering very well.

adhisadi commented 1 month ago

Can you provide gene expression matrix for this dataset or add an option to perform batch correction using Seurat's integrated.ccca method instead of Harmony? I process my dataset using integrated.cca batch correction.

It makes sense that the ref and query needs to be processed the same way but when I project back the prediction to my UMAP, the predictions don't fit my UMAP structure and clustering very well.

Hi, Did you figure this out?