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Shians / Glimma

Glimma R package
GNU Lesser General Public License v3.0
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top option does not change glMDSPlot results #138

Closed mueggeb closed 6 years ago

mueggeb commented 7 years ago

First, the package is incredibly useful and very well documented. Thank you!

My issue is that the output from glMDSPlot does not change regardless of the value passed to option -top. I'm using Glimma version 1.4.0

Loaded rnaseq and groups exactly as in Figure 2 of the vignette

This recreates Figure 2 of the vignette as expected

glMDSPlot(rnaseq, groups=groups)

Each of these images is exactly the same as Figure 2.

glMDSplot(rnaseq,top=2,groups=groups) glMDSPlot(rnaseq, top=5, groups=groups) glMDSPlot(rnaseq, top=5000,groups=groups)

Similarly, gene.selection="common" does not seem to change the results

glMDSPlot(rnaseq, gene.selection = "common", groups=groups)

Shians commented 7 years ago

Thanks for the report, I know about this and it's similar to #133. I think I've actually fixed this but ended up breaking something in my vignette, so the build is broken until I can figure out how to fix my vignette.

mueggeb commented 7 years ago

Thanks for letting me know. The package is really great, we will definitely use it and cite in our research. I’ll watch for the next stable release.

From: Shian Su notifications@github.com Reply-To: Shians/Glimma reply@reply.github.com Date: Wednesday, August 23, 2017 at 8:00 AM To: Shians/Glimma Glimma@noreply.github.com Cc: "Muegge, Brian" mueggeb@wustl.edu, Author author@noreply.github.com Subject: Re: [Shians/Glimma] top option does not change glMDSPlot results (#138)

Thanks for the report, I know about this and it's similar to #133https://github.com/Shians/Glimma/issues/133. I think I've actually fixed this but ended up breaking something in my vignette, so the build is broken until I can figure out how to fix my vignette.

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