Very Sorry for the instinctive bad comment... I didn't express correctly what I meant. I meant that I would have never expected such behaviour, by default (but may be I am wrong and most of the people need quoting, and hence has sense to put it by default)
Problem solved, Philipp guessed right. It was just a quoting problem on the gene description. The problem could be solved simply adding the (quote="") parameter to the read.table command. The quoting problem reversed into that strange behavior when I merged two table (I don't know why). Thankyou very much for the assistance, Now that I realized that the quoting exists I can enjoying using R (that as a tool perfectly suits my needs at the moment). Have a nice day, Andrea On Mon, Jul 18, 2011 at 7:36 PM, David Winsemius <dwinsem...@comcast.net> wrote: > > On Jul 18, 2011, at 11:10 AM, Andrea Franceschini wrote: > >> 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. > > When I read this I thought it was an example of a young person just starting > their education exhibiting Piaget's "preoperational" stage when applied to > the task of learning a computer language. > > "the child begins to use symbols to represent objects. Early in this stage > he also personifies objects. [snipped] His thinking is influenced by > fantasy -- the way he'd like things to be -- and he assumes that others see > situations from his viewpoint." > > [Copied from a webpage for grade school teachers: > http://www2.honolulu.hawaii.edu/facdev/guidebk/teachtip/piaget.htm ] > > But when I do a search in PubMed, I find that you may be an established > researcher, so I thing the onus is now on you to demonstrate how R's > behavior is different than the documented design goals for the read.table > function. > >> 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 ??? > > I thought Pagel already gave you the answer, but your response is too > general to be sure. What exactly did you find and can you provide a minimal > code and data example that illustrates how read.table is acting in any way > different than the documentation describes? > > -- > David. > > >> 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. > > David Winsemius, MD > West Hartford, CT > > ______________________________________________ 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.
