[R] PAMR package question: How to plot Estimated probabilities for the training data and test data

Waverley waverley.paloalto at gmail.com
Tue Apr 1 23:54:35 CEST 2008


 I have tried some time trying to figure out how to use pamr to plot multiclass
 Estimated probabilities for the training data  and test data?

 Specifically, how to recreate the PAMR publication on PNAS with
 Tibshrani et al.  The publication is as attached.  The plot I want to
 do is Figure 5.

 I have downloaded the pamr package and the function which gives
 similar plot is pamr.plotcvprob  but this is different from plot
 estimated probability.

 There is one function pamr.xl.plotcvprob.compute  sounds like the one
 I am looking for but it is internal function and is not supposed to be
 called by user.

 Any R guru or expression analysis guru who are familiar with pamr can help me?

 Given saying that, I hope pamr author can make a public function to
 plot this like the figure 5 in their PNAS paper.   After they should
 encourage user to recreate their nice work through easy APIs.


 Waverley @ Palo Alto

Waverley @ Palo Alto

More information about the R-help mailing list