Batch Corrected Count Matrix

[Ethan-Earlie]

Hello, would it be possible to make the batch corrected count matrix used to generate the main UMAPs publicly available? This would be very helpful for analyzing the effect different batch correction methods have on the data and for computing a nearest neighbors graph for the corrected data.

Thank you!

[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!