Question: Why is the significance threshold on my cummeRbund volcano plot so high?
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gravatar for keisha.carlson
5.4 years ago by
United States
keisha.carlson0 wrote:

Hi,

I recently used the Tuxedo package to analyze RNA-seq data of four conditions each with four biological replicates. The Cuffdiff output .diff files indicate I have >2000 significantly differentially regulated genes. When I try to make a volcano plot using all the defaults in cummeRbund, there are only a few significant (red) points way up at the top of the figure (-log10(p value) >15). If I specifically add alpha=0.05, which is supposed to be the default, there are no longer significant points. Similarly in the scatterplot, if I use the colorByStatus = TRUE option, none of the points are colored. Does anyone have any suggestions?

Thanks so much,

Keisha

rna-seq R • 2.7k views
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