Extract x and y values from plotDispEsts
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LiZ • 0
@liz-12274
Last seen 5.7 years ago
USA

Hi, 

I am trying to extract the x and y values from plotDispEsts(dds) plot. Someone know how to do it?

Thanks

LiZ

R deseq2 • 458 views
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@mikelove
Last seen 4 hours ago
United States

See the section of the vignette, "Access to all calculated values".

The x is mcols(dds)$baseMean. The y axis is the dispersion values. There are 3 dispersion estimates plotted: dispersionsGeneEst, dispersionsFitted, and dispersions (the final estimate).

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Thank you for the prompt reply. 

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I read the vignette, "Access to all calculated values" but it is still not clear to me how to get the dispersion values. mcols(dds)$dispGeneEst should give me the dispersion per gene (black dots), right? I would like to highlight some specifics gene in the plot, but the range of values between mcols(dds)$dispGeneEst and what I see in the plot does not match. Thank you again.

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The plot uses log=“xy”. Perhaps this is the difference you are seeing?

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