Re: [Rd] read.table() can't read in this table (But Splus can) (PR#9687)

From: <marc_schwartz_at_comcast.net>
Date: Tue, 15 May 2007 09:06:51 +0200 (CEST)


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



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