On Mon, 2007-05-14 at 23:41 +0200, [EMAIL PROTECTED] 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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