I have multiple libraries of 10x Chromium single-cell RNA-seq data, which I'd like to combine. One option is using
cellranger aggr which by default does a depth normalization:
mapped: (default) Subsample reads from higher-depth libraries until they all have an equal number of confidently mapped reads per cell.
raw: Subsample reads from higher-depth libraries until they all have an equal number of total (i.e. raw, mapping-independent) reads per cell.
none: Do not normalize at all.
The new version of
Seurat (2.0) provides another way via the
These have the arguments:
do.logNormalize whether to normalize the expression data per cell and transform to log space. total.expr scale factor in the log normalization do.scale In email@example.com, perform row-scaling (gene-based z-score) do.center In firstname.lastname@example.org, perform row-centering (gene-based centering)
I'm wondering how do these methods compare? What are the pros/cons etc? What do we need to consider when we combine samples?