top option does not change glMDSPlot results

[mueggeb]

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]

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]

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 #133<#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. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#138 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AdxOa5J379vN8JnKuQYQ4r8FFMQkv0Klks5sbCJzgaJpZM4O9fML>.

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