fetching columns from another file

-----Original Message-----
From: r-help-bounces at r-project.org 
[mailto:r-help-bounces at r-project.org] On Behalf Of Amit
Sent: Sunday, January 24, 2010 10:48 AM
To: r-help at r-project.org
Subject: [R] fetching columns from another file

Hi! All,

I am trying to fetch rows from a data frame which matches to first 2
columns of another data frame. Here is the example what I am trying to
do:

ptable=read.table(file="All.txt",header=T,sep="\t")
ptable=as.matrix(ptable)
dim(ptable)

[1] 9275    6

head(ptable)

     Gene1       Gene2       PCC         PCC3        PCC23    
   PCC123
[1,] "3813_f_at" "3884_f_at" "0.9956842" "0.9955455" 
"0.9956513" "0.9956171"
[2,] "3884_f_at" "3813_f_at" "0.9956842" "0.9955455" 
"0.9956513" "0.9956171"
[3,] "3491_f_at" "3709_f_at" "0.9952116" "0.9951588" 
"0.9951601" "0.9950864"
[4,] "3709_f_at" "3491_f_at" "0.9952116" "0.9951588" 
"0.9951601" "0.9950864"
[5,] "3371_f_at" "3594_f_at" "0.9946206" "0.9945342" 
"0.9946246" "0.9946592"
[6,] "3594_f_at" "3371_f_at" "0.9946206" "0.9945342" 
"0.9946246" "0.9946592"

table=read.table(file="All_GPYeast_m.txt",header=T,sep="\t")
table=as.matrix(table)
dim(table)

[1] 9275    6

head(table)

     Gene1       Gene2       PCC         PCC3        PCC23    
   PCC123
[1,] "3491_f_at" "3709_f_at" "0.9953142" "0.9950756" 
"0.9954676" "0.9952902"
[2,] "3709_f_at" "3491_f_at" "0.9953142" "0.9950756" 
"0.9954676" "0.9952902"
[3,] "3813_f_at" "3884_f_at" "0.9951781" "0.9953901" 
"0.9959256" "0.9958152"
[4,] "3884_f_at" "3813_f_at" "0.9951781" "0.9953901" 
"0.9959256" "0.9958152"
[5,] "3371_f_at" "3594_f_at" "0.9946130" "0.9938905" 
"0.9945572" "0.9945285"
[6,] "3594_f_at" "3371_f_at" "0.9946130" "0.9938905" 
"0.9945572" "0.9945285"

Now, I wish to pick column 1&2 from 'ptable' and their coresponding
columns from 'table' and store it in a variable. I did following and
got error

PCC=apply(ptable[,c(1,2)],1,function(x)table[x[1],x[2]])

Error in FUN(newX[, i], ...) : subscript out of bounds

I was expecting something like this

head(PCC)

[1,] "3813_f_at" "3884_f_at" "0.9951781" "0.9953901" 
"0.9959256" "0.9958152"
[2,] "3884_f_at" "3813_f_at" "0.9951781" "0.9953901" 
"0.9959256" "0.9958152"
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Please, help!

regards
Amit