Dear Philipp,
You were right, thankyou very much. Effectively the second read.table didn't work (probably because of the strange characters). >From my point of view this is a very bad R bug. I precisely inserted the "\t" separator in the read table command, hence I would expect that everything is working. How can I make it work ??? Effectively there are several ' (i.e. apostrophe) characters in the file. I guess are those that confuse R Thankyou very much, Best Regards, Andrea On Mon, Jul 18, 2011 at 4:32 PM, Philipp Pagel <p.pa...@wzw.tum.de> wrote: > On Mon, Jul 18, 2011 at 04:00:29PM +0200, Andrea Franceschini wrote: >> >> I use version 13 of R in OSX (downloaded and installed less than 1 year ago). > > Probably 2.13 ... > > [...] code omitted > >> The first lines are OK (i.e. 14 columns, like the dataframe), while at >> a certain point I get lines with only 3 columns !!! >> The bad lines that contain only 3 columns have the name and the >> description of the gene (i.e. the content of the file that I merged >> with). >> Besides, these strange lines also get repeated (see the bottom). > > I havent't carefully analyzed your code so I may be wrong but my guess for > all "weird behaviour of gene related data.frames" problems is this: > > Gene descriptions love to contain things like "Foo 5' obfuscation > factor". Note the "'" in the description which read.table will > happily interpret as a quotation mark and eat lots of rows until it > happens to encouter a closing counterpart. This leads to all kinds of > funny results. So I bet your problem is not in write.table but in > reading the data. Have a closer look at your data frame: are you > really getting the expected number of observations in the merged > data.frame? Are the rows in question really ok in the data frame? If > my guess is correct you should be able to fix your problem by > including quote="" in both your read.table commands. > > If it doesn't, also try comment.char="" - another popular source of > problems. > > cu > Philipp > > -- > Dr. Philipp Pagel > Lehrstuhl für Genomorientierte Bioinformatik > Technische Universität München > Wissenschaftszentrum Weihenstephan > 85350 Freising, Germany > http://webclu.bio.wzw.tum.de/~pagel/ > ______________________________________________ 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.
