Changes between Version 27 and Version 28 of SOP/scRNA-seq


Ignore:
Timestamp:
10/06/20 18:01:36 (4 years ago)
Author:
ibarrasa
Comment:

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  • SOP/scRNA-seq

    v27 v28  
    153153  * consider each cell as a sample
    154154  * aggregate counts across all cells in a group/cluster, and treat them as one sample
    155 Seurat has 2 functions "FindAllMarkers" and "FindMarkers" that work well as long as the fold change and percentage of cells expressing the gene thresholds are not too relaxed. We recommend logfc.threshold = 0.7, min.pct = .25.).
     155Seurat has 2 functions "FindAllMarkers" and "FindMarkers" that work well as long as the fold change and percentage of cells expressing the gene thresholds are not too relaxed. We recommend logfc.threshold = 0.7, min.pct = .25. These functions by default add one pseudocount, "pseudocount.use = 1", to avoid dividing by zero. How we set this parameter, pseudocount.use, will have a strong effect on the LogFC output, especially when there are few cells in the groups compared.
    156156  * example command to compare each cluster to all other clusters:
    157157{{{