THANK YOU SO MUCH!!!!! AND THANK YOU FOR REPLYING SO QUICKLY!!! Sally ----- Original Message ----- From: "Henrik Bengtsson" <hb@stat.berkeley.edu> To: "Sally" <sagoldes at="" shaw.ca=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Monday, January 21, 2008 6:52 PM Subject: Re: [BioC] Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, > On Jan 21, 2008 5:24 PM, Sally <sagoldes at="" shaw.ca=""> wrote: >> I am using limma and am trying to set up an ExpressionSet. When I use >> the following script to read in a table of expression data (17,329 rows >> x 29 columns, tab delimited): >> >> exprdata<-read.table("exprsData.txt", header=TRUE) > > If it is a tab-delimited file, it is safer it you specify that > explicitly, i.e. use argument sep="\t". The default recognizes any > white space, e.g. if you have a "feature" with a space in the name it > will not work. > >> >> I get the following error message: >> >> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >> na.strings, : >> line 304 did not have 29 elements >> >> >> >> I looked at line 304 and it looks fine. All 29 columns have data. > > Typically the error messages are useful, so treat it as if there > indeed is a problem on that line. There might be empty spaces/tabs > etc at the end of that line. See ?read.table for options. See > especially arguments 'strip.white', 'fill', and 'comment.char'. > > Also, try to read data from the first 303 rows using argument > nrow=303. Do you get what you expect? > >> >> I have also set options(expressions=400000) >> >> Have I reached some maximum # of expressions that can be read in, or is >> it another problem? If I have reached a maximum #, is there a fix? > > That option has nothing to do with gene expression data. It deals > with syntactical R expression (think programming language). > > /Henrik > >> >> >> My exprsData.txt file looks like this (note this is not the whole >> spreadsheet) >> >> Feature c0M1 c0M2 c0M3 c0M4 >> U179971 -4.7472 -4.43814 -4.3977 -2.97843 >> e1 -0.24565 -0.53124 0.109064 -0.01936 >> e2 -0.71906 0.035403 -0.16786 0.528748 >> e3 -0.17362 0.32998 -0.0791 -0.50046 >> e4 0.065989 0.003221 -0.30596 -0.42857 >> e5 0.269098 -0.34523 -0.98694 -0.57842 >> e6 0.038301 -0.09612 0.190023 -0.10283 >> e7 -0.06462 -0.56698 -0.34373 0.285194 >> e8 -1.10146 -0.06621 0.337491 -0.1891 >> CA054869 -0.83861 0.145514 -0.40484 -0.18785 >> CB490276 -0.71377 0.569419 -0.99984 -0.51384 >> >> >> Thank you >> >> Sally Goldes >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.5.516 / Virus Database: 269.19.7/1234 - Release Date: 1/20/2008 > 2:15 PM > >