Question: Estimating cell size factors for single cell RNA-seq data
1
2.0 years ago by
gquon10
gquon10 wrote:
Hi all, I'm interested in calculating cell size factors for scRNA-seq data. The standard calculation for size factors (e.g. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8) involves computing geometric means of each gene's expression level across all cells, but this isn't practical due to the large number of zeros in scRNA-seq data. I've seen suggestions to add 1 to all counts, but wonder if there is a more rigorous, unbiased calculation.
modified 2.0 years ago by Michael Love24k • written 2.0 years ago by gquon10
Answer: Estimating cell size factors for single cell RNA-seq data
2
2.0 years ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

Check out:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0947-7

... implemented as the computeSumFactors function in scran. Make sure you read the documentation, though.

Answer: Estimating cell size factors for single cell RNA-seq data
2
2.0 years ago by
Andrew_McDavid190 wrote:

You might also try

Bacher R, Chu L, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton MA and Kendziorski C (2017). “SCnorm: robust normalization of single-cell RNA-seq data.” Nature Methodshttps://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4263.html.

Software is available in Bioconductor devel and github: https://github.com/rhondabacher/SCnorm

Answer: Estimating cell size factors for single cell RNA-seq data
2
2.0 years ago by
Michael Love24k
United States
Michael Love24k wrote:

These were the papers I was going to suggest :) Another one which looks at size factors and their relationship to zeros is this one:

http://www.biorxiv.org/content/early/2017/06/30/157982