read.table() can't read in this table (But Splus can)

On Mon, 2007-05-14 at 23:41 +0200, vax9000 at gmail.com wrote:

Full_Name: vax, 9000
Version: 2.4.0, 2.2.1
OS: 2.4.0: Mac OS X; 2.2.1: Linux
Submission from: (NULL) (192.35.79.70)


To reproduce this bug, first go to the website 

"http://llmpp.nih.gov/DLBCL/" and

download the 14.8M data set "Web Figure 1 Data file". The 

direct link is

"http://llmpp.nih.gov/DLBCL/NEJM_Web_Fig1data". Save it as 

"datafile.txt"

Then, start R, type in command "x <- 

read.table("datafile.txt", header=TRUE,

sep="\t")". The data has 7400 lines, but not all lines 

could be read in by R.

Easier test data set:
Use the command "head -n 100 datafile.txt > 

shortdatafile.txt" to extract the

first 100 lines. The R command "x <- 

read.table("datafile.txt", header=TRUE,

sep="\t")" could not read in even this 100 lines of data. 

But Splus can, with the same command. What is wrong?

Using R version 2.5.0 Patched:

DF <- 

read.table("http://llmpp.nih.gov/DLBCL/NEJM_Web_Fig1data", 
header = TRUE, sep = "\t")
Warning message:
number of items read is not a multiple of the number of columns 


So I tried it with 'fill = TRUE' and that seems to work, 
which suggests
that perhaps something is going on with the data file structure:

DF <- read.table("http://llmpp.nih.gov/DLBCL/NEJM_Web_Fig1data", 
                 header = TRUE, sep = "\t", fill = TRUE)

str(DF)

'data.frame':   4734 obs. of  295 variables:
 $ UNIQID                                     : int  27481 
17013 24751 27498 27486 30984 17293 28329 27459 27482 ...
 $ NAME                                       : Factor w/ 
4040 levels "||*AA037178|Hs.179661|FK506 binding protein 1A 
(12kD)",..: 3444 3445 3446 3444 3445 657 1788 3121 3119 3119 ...
 $ MLC94.46_LYM009_de.novo.untreated          : num  0.234 
0.452 0.405 0.115 0.249 ...
 $ MLC96.45_LYM186_de.novo.untreated          : num  -0.1725 
-0.0387 -0.0413 -0.0242 -0.1028 ...
 $ MLC91.27_LYM427_de.novo.untreated          : num  0.200 
0.175 0.195 0.223 0.179 ...
 $ MLC96.84_LYM225_transformed                : num  -0.213 
-0.325 -0.200 -0.199 -0.155 ...
 $ MLC95.43_LYM095_de.novo.untreated          : num  -0.1197  
0.0038 -0.0213 -0.0705 -0.0755 ...
 $ MLC91.28_LYM428_de.novo.untreated          : num  -0.3729  
0.0047 -0.2220 -0.3373 -0.2808 ...
 $ MLC94.50_LYM004_de.novo.untreated          : num  -0.195 
-0.224 -0.126 -0.161 -0.199 ...
 $ MLC95.46_LYM098_de.novo.untreated          : num  0.489 
0.611 0.577 0.661 0.519 ...
 $ MLC95.62_LYM114_de.novo.untreated          : num  0.390 
0.657 0.747 0.723 0.731 ...
 $ MLC95.85_LYM137_de.novo.untreated          : num  -0.277 
-0.564 -0.297 -0.140 -0.513 ...
..


I would update your version of R and then re-try this.

HTH,

Marc Schwartz