[BioC] problem with read.table

Martin Morgan mtmorgan at fhcrc.org
Sun Jul 20 14:47:01 CEST 2008


carol white <wht_crl at yahoo.com> writes:

>                                                                               
>  t = read.table ("my_file", check.names = FALSE, header = T)                  
>  gives the same result, modifying duplicate names.                            
>  Carol                                                                        

what does sessionInfo() say (i.e., is your R current; is this
something special to your OS or LOCALE)?  Have you done this in a
'clean' R session, e.g., starting R from the shell with R --vanilla ?
And for what it's worth

> read.table("~/tmp/tmp.txt", header=TRUE, check.names=FALSE)
  AM2 AM2 AM2 FAL
1   2   3   4   5
2   1  -1  -3  -2

> sessionInfo()
R version 2.7.1 Patched (2008-07-03 r46033) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  utils     datasets  grDevices methods   base     
 
Martin

>  --- On Sat, 7/19/08, Martin Morgan <mtmorgan at fhcrc.org> wrote:               
>                                                                               
>            From: Martin Morgan <mtmorgan at fhcrc.org>     Subject: Re:          
>       [BioC] problem with read.table     To: wht_crl at yahoo.com     Cc:        
>       bioconductor at stat.math.ethz.ch     Date: Saturday, July 19, 2008,       
>       1:52 PM                                                                 
>                                                                               
>                                                                               
>       Hi Carol...                                                             
>                                                                               
>                                                                               
>  Carol white <wht_crl at yahoo.com> writes:                                      
>                                                                               
>                                                                               
>  > Hi,                                                                        
>                                                                               
>  > Although I set check.names to FALSE in read.table, the duplicate names get 
>                                                                               
>  modified. What should be done in this case?                                  
>                                                                               
>  >                                                                            
>                                                                               
>  > the text file to be read by read.table                                     
>                                                                               
>  >                                                                            
>                                                                               
>  > AM2      AM2     AM2     FAL                                               
>                                                                               
>  > 2               3                                                          
>   4                                                                           
>                                                                               
>  5                                                                            
>                                                                               
>  > 1               -1           -3        -2                                  
>                                                                               
>  >                                                                            
>                                                                               
>  > t = read.table ("my_file", check.names = F, header = T)                    
>                                                                               
>                                                                               
>  Maybe spell out TRUE, FALSE (reserved words, cannot be assigned to) to       
>                                                                               
>  avoid getting the value of variables T, F from your environment??            
>                                                                               
>                                                                               
>  Martin                                                                       
>                                                                               
>                                                                               
>  >> t                                                                         
>                                                                               
>  > AM2      AM2.1     AM2.2     FAL                                           
>                                                                               
>  >                                                                            
>                                                                               
>  > 2               3             4                                            
>                                                                               
>  5                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  > 1               -1           -3        -2                                  
>                                                                               
>  >                                                                            
>                                                                               
>  > instead of                                                                 
>                                                                               
>  >                                                                            
>                                                                               
>  > AM2      AM2     AM2    FAL                                                
>                                                                               
>  >                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  > 2               3             4                                            
>                                                                               
>  5                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  > 1               -1           -3        -2                                  
>                                                                               
>  >                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  > Best,                                                                      
>                                                                               
>  > carol                                                                      
>                                                                               
>  >                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  >                                                                            
>                                                                               
>  >   [[alternative HTML version deleted]]                                     
>                                                                               
>  >                                                                            
>                                                                               
>  > _______________________________________________                            
>                                                                               
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>                                                                               
>                                                                               
>  --                                                                           
>                                                                               
>  Martin Morgan                                                                
>                                                                               
>  Computational Biology / Fred Hutchinson Cancer Research Center               
>                                                                               
>  1100 Fairview Ave. N.                                                        
>                                                                               
>  PO Box 19024 Seattle, WA 98109                                               
>                                                                               
>                                                                               
>  Location: Arnold Building M2 B169                                            
>                                                                               
>  Phone: (206) 667-2793                                                        
>                                                                               
>
>

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793



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