R help - Oct 2006 - why it returns list level number instead of its content?

for example:
I have a data frame.
data$V4 returns:
.....
[6936] P05796       P11096       P76174       P04475       P18775
[6941] P33225       P76387       P76388       P76388       P09375
[6946] P15300       P15723
1375 Levels:  O50190 O65938 O69415 P00274 P00363 P00364 P00370 P00373 ...
Q9AJ15
data$V5 returns something like data$V4
I want to cbind this two columns, so I use
new <- cbind(data$V4,data$V5)
I expect it to return something like:
[1] P05761 P11986
[2] .......
however it returns
[1] 215 434
[2] 134 213
.............
it uses level number instead of  its content like "P05761". What's
wrong
with  it?  how can I get its content instead of level number? I can use some
dirty ways to do that but I didn't understand why.

	[[alternative HTML version deleted]]

The class "factor" is defined for vectors, not matrices.
The attempt to use a factor in a matrix setting coerces it to numeric.
See the documentation for factor where it says
"In particular, as.numeric applied to a factor is meaningless,
and may happen by implicit coercion."
> tmp <- matrix(1:8, 4)
> tmp
     [,1] [,2]
[1,]    1    5
[2,]    2    6
[3,]    3    7
[4,]    4    8
> factor(tmp)
[1] 1 2 3 4 5 6 7 8
Levels: 1 2 3 4 5 6 7 8
> 

## A simplified example based on yours:
> tmp <- data.frame(a=factor(letters[1:4]), b=factor(letters[5:8]))
> tmp
  a b
1 a e
2 b f
3 c g
4 d h
> cbind(tmp$a, tmp$b)  ## coerced to numeric, both factors went to 1:4
     [,1] [,2]
[1,]    1    1
[2,]    2    2
[3,]    3    3
[4,]    4    4
> tmp[, c("a","b")]  ## in your example, subscripting is
probably the right method
  a b
1 a e
2 b f
3 c g
4 d h
> cbind.data.frame(tmp$a, tmp$b)  ## explicit use of cbind.data.frame works.
  tmp$a tmp$b
1     a     e
2     b     f
3     c     g
4     d     h

Rich

You have read in the data as factors. 
 Try class(data$V4) to see this.

When you are doing something like a cbind R treats the
factors as numbers.  You need to convert the factors
back to character data. 
 Try something like d1 <- as.character(data$V4) d2 <-
as.character(data$V5) and then do a cbind to 
see what happens.  

This is not the proper way to do things, I'm sure, but
it should help you see what is happening.    

--- Hu Chen <chencheva at gmail.com> wrote:
> for example:
> I have a data frame.
> data$V4 returns:
> .....
> [6936] P05796       P11096       P76174       P04475
>       P18775
> [6941] P33225       P76387       P76388       P76388
>       P09375
> [6946] P15300       P15723
> 1375 Levels:  O50190 O65938 O69415 P00274 P00363
> P00364 P00370 P00373 ...
> Q9AJ15
> data$V5 returns something like data$V4
> I want to cbind this two columns, so I use
> new <- cbind(data$V4,data$V5)
> I expect it to return something like:
> [1] P05761 P11986
> [2] .......
> however it returns
> [1] 215 434
> [2] 134 213
> .............
> it uses level number instead of  its content like
> "P05761". What's wrong
> with  it?  how can I get its content instead of
> level number? I can use some
> dirty ways to do that but I didn't understand why.
> 
> 	[[alternative HTML version deleted]]
> 
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