Batch Corrected Count Matrix about brca_cell_atlas

[Ethan-Earlie]

Or, if the expression data was not corrected - would it be possible to shared the corrected PCs that were used to produce the published UMAP?

[sunnyzwu]

Hi Ethan, we used Seurat's anchor based data integration method and thus, there is not a complete batch corrected matrix available for our dataset. For reproducing the UMAPs in the paper, you should be able to download the UMAP coordinates (tsv files - https://singlecell.broadinstitute.org/single_cell/study/SCP1039/a-single-cell-and-spatially-resolved-atlas-of-human-breast-cancers#study-download) on the broad portal for each of the classes of cells (all cells, epithelial, myeloid, stromal etc.). Hope that helps!

[Ethan-Earlie]

Hi Sunny, thank you for your response - this is helpful. Rather than a batch corrected matrix, would it be possible to share the resulting PCA matrix after data integration? I am trying to implement nearest neighbor graph based methods, which are dependent on PCs rather than UMAP coordinates.

Thank you!