[R] read.table & readLines behaviour?

[J.delasHeras at ed.ac.uk]

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
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