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Old 06-17-2014, 01:45 PM   #1
Location: Philadelphia

Join Date: May 2012
Posts: 19
Default What to do with genes with very low counts in a dataset

Hi all,
I have a dataset from a single cell RNASeq project and there are many genes with very few counts (1 or 2 in a few samples) in the data set. While this is important info (tells us that these genes are not expressed), how would one handle them for a differential expression analysis (I use DESeq2)? Should I delete them or keep them? For me this means the difference between having a dataset with either ~17000 genes or ~11,500 genes (if I exclude genes with an average count less than 3).
Thanks for your thoughts on this!
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Old 06-17-2014, 02:18 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

DESeq2 will filter them out for you, you needn't do it manually.
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Old 06-17-2014, 04:37 PM   #3
Michael Love
Senior Member
Location: Boston

Join Date: Jul 2013
Posts: 333

Devon's always got the right answer

If you want to know more about filtering out genes with few counts, we have a section on this (independent filtering) in the "Theory" part of the DESeq2 vignette.

A reference on independent filtering:

Bourgon R, Gentleman R, Huber W.
"Independent filtering increases detection power for high-throughput experiments."
Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-51. doi: 10.1073/pnas.0914005107. Epub 2010 May 11.
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Old 06-18-2014, 07:59 AM   #4
Location: Philadelphia

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Thanks for the quick replies, dpryan and Michael Love!
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