read.table & readLines behaviour?
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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