[R] problems with which

[Nicola Spotorno]

Dear all,
I'm quite new in R and I have a problem with the function which. When I 
use it to select a subset of a dataframe it works well but somewhere R 
takes trace of the past dataframe and this creates problems with 
following operations.
For example:

sentences <- read.xls("frasi.tot.march.3.xls", header=TRUE)

head(sentences)
  fam subjID Cond  Code reg     total     first    second
1   f     30   an fDan1   1 0.2812500 0.2812500 0.0000000
2   f     30   an fDan1   2 1.7851562 0.5390625 1.2460938
3   f     30   an fDan1   3 1.2304688 0.6679688 0.5625000
4   f     30   an fDan1   4 0.6289062 0.4375000 0.1914062
5   f     30   an fDan2   1 0.1367188 0.1367188 0.0000000
6   f     30   an fDan2   2 0.8632812 0.6679688 0.1953125

str(sentences)
'data.frame':    4799 obs. of  8 variables:
 $ fam   : Factor w/ 2 levels "f","uf": 1 1 1 1 1 1 1 1 1 1 ...
 $ subjID: int  30 30 30 30 30 30 30 30 30 30 ...
 $ Cond  : Factor w/ 4 levels "an","fi","le",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ Code  : Factor w/ 126 levels "fAan1","fAan2",..: 72 72 72 72 73 73 73 
73 74 74 ...
 $ reg   : int  1 2 3 4 1 2 3 4 1 2 ...
 $ total : num  0.281 1.785 1.23 0.629 0.137 ...
 $ first : num  0.281 0.539 0.668 0.438 0.137 ...
 $ second: num  0 1.246 0.562 0.191 0 ...

# If you look the variable "Cond" you see that it has 4 levels

sentences_trial <- sentences[which(sentences$Cond!= "an"),]

 > str(sentences)
'data.frame':    4799 obs. of  8 variables:
 $ fam   : Factor w/ 2 levels "f","uf": 1 1 1 1 1 1 1 1 1 1 ...
 $ subjID: int  30 30 30 30 30 30 30 30 30 30 ...
 $ Cond  : Factor w/ 4 levels "an","fi","le",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ Code  : Factor w/ 126 levels "fAan1","fAan2",..: 72 72 72 72 73 73 73 
73 74 74 ...
 $ reg   : int  1 2 3 4 1 2 3 4 1 2 ...
 $ total : num  0.281 1.785 1.23 0.629 0.137 ...
 $ first : num  0.281 0.539 0.668 0.438 0.137 ...
 $ second: num  0 1.246 0.562 0.191 0 ...

# Now variable "Cond" still has 4 levels but with which I have excluded 
one level!
#Whether  I apply at this point  interaction plot, the graph considers 4 
levels of which.

attach(sentence_trial)
x11()
interaction.plot(Cond,fam,total)

# Where is the problem?

Thanks in advance.

Nicola