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