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Shians / Glimma

Glimma R package
GNU Lesser General Public License v3.0
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make glMDSPlot.DGEList's default prior.count = 2 #173

Closed jdrnevich closed 5 years ago

jdrnevich commented 5 years ago

edgeR's plotMDS.DGEList changed the default value of prior.count from 0.25 to 2. It took me a while to figure out why glMDSPlot.DGEList was giving me a different clustering with what I thought was the same call. I propose changing glMDSPlot.DGEList's default for prior.count to 2 as well. I don't know if there are any other functions with the prior.count argument...

Shians commented 5 years ago

Thanks again Jenny! That's a pretty dramatic change in prior count, I wonder what the reasoning for it is.

jdrnevich commented 5 years ago

You're welcome! See https://support.bioconductor.org/p/114934/ for a discussion on the change

codecov-io commented 5 years ago

Codecov Report

Merging #173 into master will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #173   +/-   ##
=======================================
  Coverage   92.51%   92.51%           
=======================================
  Files          18       18           
  Lines        1310     1310           
=======================================
  Hits         1212     1212           
  Misses         98       98
Impacted Files Coverage Δ
R/glMDSPlot.R 92.3% <ø> (ø) :arrow_up:

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