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Problem: DE genes search on initial step of SAVER removes rear landmark genes, making impute step useless.
Idea to consider: seurat's DE genes binned search
Possible solution: we have no prior information about real landmark genes and full dropout correction is time-consuming, possible solution is to group genes by nZero percentage, making assumption, that zeroes are mainly real zeroes, rather dropout events
The text was updated successfully, but these errors were encountered:
This isn't optimal, but as we know, "real" dropouts are around 10-25% for droplet-based methods.
Limiting Saver's lasso with genes in these boundaries we can dramatically improve performance on "10k+ genes" datasets
We assume, that correction may perform better in case of several expression levels of the same gene.
E.g. Nanog fold-change is 4-8 orders for 4cell->blastocyst and 1.5-3 for subpopulations.
If there is a gene that co-expressed with Nanog in the first subpopulation and not expressed in the second it can be imputed, indusing false-positives.
Problem: DE genes search on initial step of SAVER removes rear landmark genes, making impute step useless.
Idea to consider: seurat's DE genes binned search
Possible solution: we have no prior information about real landmark genes and full dropout correction is time-consuming, possible solution is to group genes by nZero percentage, making assumption, that zeroes are mainly real zeroes, rather dropout events
The text was updated successfully, but these errors were encountered: