Question: Normalisation of reference dataset for scRNA cell type annotation
gravatar for user31888
15 months ago by
United States
user3188880 wrote:

I have scRNA data in a form of a SingleCellExperiment object that I previously filtered, normalised, clustered, with genes selected.

I am trying to assign a cell type to each of my cells in this SingleCellExperiment object using scmap (here) and the Human Primary Cell Atlas (HPCA) as a reference (taken from the SingleR package).

Following the scmap vignette, I created a SingleCellExperiment object out of the HPCA dataset, selected features and created indexes.

I am now ready to project my scRNA data into these indexes.

However, is it correct to project scRNA read counts (or CPM) on HPCA reference indexes knowing that HPCA came from affymetrix data normalized differently (HPCA values are robust multi-array average (RMA) expression measure)?

ADD COMMENTlink written 15 months ago by user3188880

I would be a bit skeptical to annotate single cell data using bulk RNA data generated from primary cells that too by using arrays. It may not work. Why don't you use marker genes to annotate the cells ?

ADD REPLYlink modified 15 months ago • written 15 months ago by geek_y11k

Do you mean using cell type signatures and scoring their enrichment with GSEA or gsva for example?

ADD REPLYlink written 15 months ago by user3188880

by using expression of well known marker genes per cell type.

ADD REPLYlink written 15 months ago by geek_y11k

I came across this recent database, CellMarker. Do you think a simple GSVA using this database could be accurate? I need to get a score of some sort to be able to discriminate cell types.

ADD REPLYlink written 15 months ago by user3188880
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