From andy_liaw at merck.com  Tue May 15 15:11:58 2007
From: andy_liaw at merck.com (Liaw, Andy)
Date: Tue, 15 May 2007 09:11:58 -0400
Subject: [Rd] read.table() can't read in this table (But Splus can)
In-Reply-To: <20070515070651.0A60C485BF@slim.kubism.ku.dk>
References: <20070515070651.0A60C485BF@slim.kubism.ku.dk>
Message-ID: <39B6DDB9048D0F4DAD42CB26AAFF0AFA04293A5A@usctmx1106.merck.com>

It's the quoting character(s).  This following seems to read the file in
correctly:

R> DF <- read.table("http://llmpp.nih.gov/DLBCL/NEJM_Web_Fig1data", 
+                   header = TRUE, sep = "\t", quote="")
R> str(DF)
'data.frame':   7399 obs. of  295 variables:
[...]

If I have to guess, it's the "3-prime" or "5-prime" that occurs commonly
in biology...

I don't think Mr. 9000 Vax can blame R for this.

Best,
Andy
 

From: marc_schwartz at comcast.net
> 
> 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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 
> 


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[Rd] read.table() can't read in this table (But Splus can)
Liaw, Andy