Question: How are Outliers determined in DEseq2?
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gravatar for john.perish
2.2 years ago by
john.perish0 wrote:

How are outliers determined in DEseq2?

I have aligned my samples using STAR and did differential expression analysis with DEseq2. In the output there are options to view different "statuses." Low (Mean count value less than 10), OK (Mean count value higher than 10), and Outlier.

It is not entirely clear how Outliers are determined. Does anyone know?

I have used multiple alignment and differential expression analyses and this pipeline yields the smallest number of significant genes in DE. But many of the genes that show up in the Outliers list are significant in other analyses.

Thanks!

rna-seq star deseq2 • 1.1k views
ADD COMMENTlink modified 2.2 years ago by Devon Ryan94k • written 2.2 years ago by john.perish0
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gravatar for Devon Ryan
2.2 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

DESeq2 uses Cook's distance, provided you have sufficient replicates. You can tweak the cutoff used with the cooksCutoff option to results().

ADD COMMENTlink written 2.2 years ago by Devon Ryan94k
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