[R] read.table & readLines behaviour?

[J.delasHeras at ed.ac.uk]

The result was 11, 24001 times, as I expected originally. hmmm...

JOse


Quoting Gabor Grothendieck <ggrothendieck at gmail.com>:

> Try looking at the result of count.fields to diagnose it.
>
> On Tue, Sep 23, 2008 at 5:19 AM,  <J.delasHeras at ed.ac.uk> 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: J.delasHeras at ed.ac.uk
>> 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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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>



-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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.