I am running RankProd on a microarray experiment with 3 arrays, 2 of
which are dye-swaps.

 

library(RankProd) 

#The data is an MA object as used in limma. 

#The first two arrays are dye swaps, so I flip them around.

data.rp<-cbind(-1*MA.ets$M[,1:2],MA.ets$M[,3])

gnames<-MA.ets$genes$GeneName #in case I want to use gene names 

gnums=seq(1,nrow(data.rp))    #in case I want to just use gene.index
numbers

cl=c(1,1,1)                   #Simple one class design 

RP.ets<-RP(data.rp,cl,logged=T,rand=083006)

plotRP(RP.ets,cutoff=.05)

topGene(RP.ets,num.gene=20,logged=T,logbase=2,gene.names=t(gnums))

 

The problem is, my plots are totally red at a cutoff of .05, though they
are shaped like RP plots I have done in the past, and my topGenes table
isn't sorted in any order. Here are the top few from each table.

 

$Table1

      gene.index    RP/Rsum FC:(class1/class2)    pfp P.value

41029      41029 10380.3988             0.8927 1.1024  0.2143

5767        5767    14.4609             0.1492 0.0000  0.0000

1576        1576    29.2713             0.1873 0.0000  0.0000

789          789    48.4029             0.2193 0.0000  0.0000

34142      34142 17623.7764             0.9945 1.0647  0.5229

41440      41440 22461.8948             1.0502 1.0102  0.7160

1284        1284    80.7459             0.2682 0.0057  0.0000

...

 

$Table2

      gene.index    RP/Rsum FC:(class1/class2)    pfp P.value

2621        2621    67.5055             3.2622 0.0200  0.0000

11728      11728    78.8400             3.9658 0.0150  0.0000

19855      19855    93.8845             2.9963 0.0167  0.0000

24904      24904 18891.3612             1.0178 1.0341  0.5768

17221      17221   130.7084             2.7639 0.0220  0.0000

28383      28383 19821.5391             0.9914 1.0246  0.6149

5413        5413   150.8104             2.6640 0.0200  0.0000

...

 

Since the table isn't sorted right and the plots are fishy, I don't
trust the pfp's or pvalues. Should I? Am I doing something wrong? 

 

Other information:

> sessionInfo()

Version 2.3.1 (2006-06-01) 

i386-pc-mingw32 

 

attached base packages:

[1] "methods"   "stats"     "graphics"  "grDevices" "utils"
"datasets"  "base"     

 

other attached packages:

  marray    limma RankProd 

"1.10.0"  "2.7.5"  "2.4.0"

 

 

Thanks a lot for the help,

 

Cody Olsen

Hunstman Cancer Institute

University of Utah

cody.olsen@hci.utah.edu


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