Question

Overdispersion for single cell RNA seq experiments

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6.8 years ago

ly.leifels • 0

How can I deal with overdispersion in single-cell RNA seq experiments? especially regarding low counts?

scRNASeq overdispersion • 2.1k views

ADD COMMENT • link updated 6.2 years ago by eric.kern13 ▴ 240 • written 6.8 years ago by ly.leifels • 0

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For clustering, or differential expression, or something else entirely?

ADD REPLY • link 6.8 years ago by Devon Ryan 104k

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for clustering genes into gene modules

ADD REPLY • link 6.8 years ago by ly.leifels • 0

score 1 · Answer 1 · 2018-02-05

What have you tried so far? One sensible solution might be to try:

whatever you would try if you didn't have to worry about low counts; maybe K-means
some out-of-the-box method such as PAGODA. http://hms-dbmi.github.io/scde/pagoda.html

If those don't get you to where you need to be, then where's the gap? Do you think the estimates are off, and if so, why? Or maybe you just need more reliable quantification of uncertainty?