The result was 11, 24001 times, as I expected originally. hmmm...
JOse
Quoting Gabor Grothendieck <[EMAIL PROTECTED]>:
Try looking at the result of count.fields to diagnose it.
On Tue, Sep 23, 2008 at 5:19 AM, <[EMAIL PROTECTED]> wrote:
Hi,
I have been using 'read.table' regularly to read tab-delimited text files
with data. No problem, until now.
Now I have a file that appeared to have read fine, and the data inside looks
correct (structure etc), except I only had 15000+ rows out of the expected
24000. Using 'readLines' instead, and breaking up the data by tabs, gives me
the expected result.
I do not understand why this is happening and I can't find anything obvious
in the data to explain the bahaviour...
Does anybody have an explanation? something to watch out for?
If I run this I get the incomplete set:
oldprobesets<-read.table("All_norm_calls.txt",sep="\t",header=T,stringsAsFactors=F)
dim(oldprobesets)
[1] 15733 11
but I get the right data if I use:
probesets<-readLines("All_norm_calls.txt")
tmp<-matrix(ncol=11,nrow=24000)
for (i in 1:24000) tmp[i,]<-unlist(strsplit(probesets[i+1],split="\t"))
colnames(tmp)<-unlist(strsplit(probesets[1],split="\t"))
probesets<-data.frame(tmp,stringsAsFactors=F)
dim(probesets)
[1] 24000 11
Here's my sessionInfo output:
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils methods
[8] base
other attached packages:
[1] limma_2.14.0 svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59 svMisc_0.9-5
[6] svIDE_0.9-5
loaded via a namespace (and not attached):
[1] tools_2.7.0
Thanks!
Jose
--
Dr. Jose I. de las Heras Email: [EMAIL PROTECTED]
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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--
Dr. Jose I. de las Heras Email: [EMAIL PROTECTED]
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
