Question

Estimating cell size factors for single cell RNA-seq data

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gquon ▴ 10

@gquon-13705

Last seen 7.3 years ago

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.

scrnaseq rnaseq normalization DESeq2 • 3.4k views

ADD COMMENT • link updated 7.3 years ago by Michael Love 43k • written 7.3 years ago by gquon ▴ 10

score 2 · Accepted Answer · 2017-08-10

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Aaron Lun ★ 28k

@alun

Last seen 33 minutes ago

The city by the bay

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.

ADD COMMENT • link 7.3 years ago Aaron Lun ★ 28k

score 2 · Accepted Answer · 2017-08-10

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 Methods. https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4263.html.

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

score 2 · Accepted Answer · 2017-08-10

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Michael Love 43k

@mikelove

Last seen 16 hours ago

United States

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

ADD COMMENT • link 7.3 years ago Michael Love 43k