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Question: Estimating cell size factors for single cell RNA-seq data
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gravatar for gquon
11 months 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.
ADD COMMENTlink modified 11 months ago by Michael Love18k • written 11 months ago by gquon10
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gravatar for Aaron Lun
11 months ago by
Aaron Lun20k
Cambridge, United Kingdom
Aaron Lun20k 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.

ADD COMMENTlink written 11 months ago by Aaron Lun20k
2
gravatar for Andrew_McDavid
11 months ago by
Andrew_McDavid130 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

ADD COMMENTlink written 11 months ago by Andrew_McDavid130
2
gravatar for Michael Love
11 months ago by
Michael Love18k
United States
Michael Love18k 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

ADD COMMENTlink written 11 months ago by Michael Love18k
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