plotMDS: metric or non-metric method?
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@marthanigg1-8520
Last seen 8.7 years ago
Canada

Hi all,

maybe my question is a silly one but I'm wondering which algorithm is used to produced MDS plot (plotMDS function) in EdgeR package : classical, metric or non-metric ?? My guess is a classical one since it is a variation of the Principal Coordinate Analysis, however, I'm not sure at all.

Can anyone help me?

Thank you

Martha

edger rnaseq • 953 views
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@james-w-macdonald-5106
Last seen 13 hours ago
United States

There is a hint in the help page:

Value:

     A plot is created on the current graphics device.

     An object of class  "MDS"  is invisibly returned. This is a list
     containing the following components:

distance.matrix: numeric matrix of pairwise distances between columns
          of  x

cmdscale.out: output from the function  cmdscale  given the distance
          matrix

And cmdscale() is the function that does the Classical Multidimensional Scaling.

 

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@marthanigg1-8520
Last seen 8.7 years ago
Canada

Thanks!! Now I understand!

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