[R] Rank Product

Nadege Nana
2006-01-22T11:55:43Z

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:

  -          How can I determine which class is  the class of up-regulated genes
and which to the down regulated gene

  -          How can i interpret the results :

  $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

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  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
………………………………………………...


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