[R] Rank Product

From: Nadege Nana <perlenana_at_yahoo.fr>
Date: Sun 22 Jan 2006 - 22:55:43 EST


  Hello Guys,
  I'm using the package RankProduct to determine the differential expression of genes in 2 classes.   The importance of the thing is to know:    

$pfp, $RPs, $RPrank,
   

  Orirank,
$Orirank$"class1 > class 2"
$Orirank$"class1 < class 2"
   

   $AveFC    

  Table1: Genes called significant under class1 < class2   Table2: Genes called significant under class1 > class2        

  Thanks for your help.    

  Example:    

  Formula:
  RP.out<-RP(data, pt.cl, g.names, num.perm = 100, logged = TRUE,    na.rm = FALSE, plot = FALSE, rand =123)                                                                                                             

$pfp

      class1 < class2 class1 > class 2
  1        0.97115385      0.002000000
   
   

$RPs
class1 < class2 class1 > class 2 1 37.54242 21.63239
$RPrank
class1 < class2 class1 > class 2 1 26.0 5.0

  Orirank
$Orirank$"class1 < class2"

          [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]

  ..
    

$Orirank$"class1 > class 2"

  ..          

$AveFC

      log/unlog(class1/class2)
  1               0.0694052288
  
     
      
  #Genes by controlling pfp <0.05    
                                                                                                                                                                                                                                    &nbsp;                                                                                                                                                                                                                                                               &nbsp;                                                                                                                                                                                                                                                               &nbsp;                                                                                                                                                                                                                                         !
          
             &nbsp;                                                                                                                                                                                                                                                               &nbsp;                                                                                                                                                                                                                                                               &nbsp;                                                                                                                                                                                                                
  topGene(RP.out, cutoff = 0.05, logged = TRUE, logbase = 2, g.names)    

  Table1: Genes called significant under class1 < class2        

  Table2: Genes called significant under class1 > class2        

$Table1

             gene.index RP/Rsum FC:(class1/class2)    pfp
  Gen n             51 15.8595             0.8204 0.0000
  Gen n-1          65 18.3764             0.9582 0.0250
  Gen n-2         75 18.6893             0.8916 0.0167
  Gen n-3             52 19.0778             0.8928 0.0150
  .
   

$Table2
gene.index RP/Rsum FC:(class1/class2) pfp Gen n-3 98 10.0913 1.4331 0.0000 Gen n-2 39 15.2657 1.4062 0.0000 Gen n-1 2 19.8796 1.1414 0.0000 Gen n 97 20.3225 1.1446 0.0000 ... --------------------------------- [[alternative HTML version deleted]]

______________________________________________

R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sun Jan 22 23:04:36 2006

This archive was generated by hypermail 2.1.8 : Mon 23 Jan 2006 - 02:19:15 EST