t = read.table ("my_file", check.names = FALSE, header = T) gives the same result, modifying duplicate names. Carol --- On Sat, 7/19/08, Martin Morgan <mtmorgan@fhcrc.org> wrote: From: Martin Morgan <mtmorgan@fhcrc.org> Subject: Re: [BioC] problem with read.table To: wht_crl@yahoo.com Cc: bioconductor@stat.math.ethz.ch Date: Saturday, July 19, 2008, 1:52 PM Hi Carol... Carol white <wht_crl@yahoo.com> writes: > Hi, > Although I set check.names to FALSE in read.table, the duplicate names get modified. What should be done in this case? > > the text file to be read by read.table > > AM2 AM2 AM2 FAL > 2 3 4 5 > 1 -1 -3 -2 > > t = read.table ("my_file", check.names = F, header = T) Maybe spell out TRUE, FALSE (reserved words, cannot be assigned to) to avoid getting the value of variables T, F from your environment?? Martin >> t > AM2 AM2.1 AM2.2 FAL > > 2 3 4 5 > > 1 -1 -3 -2 > > instead of > > AM2 AM2 AM2 FAL > > > 2 3 4 5 > > > 1 -1 -3 -2 > > > Best, > carol > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 [[alternative HTML version deleted]]

This does not make a whole lot of sense, since read.csv is a wrapper around read.table: > read.csv function (file, header = TRUE, sep = ",", quote = "\"", dec = ".", fill = TRUE, comment.char = "", ...) read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.char, ...) <environment: namespace:utils=""> Notice the fill = TRUE argument, that is sometimes nice and sometimes catastrophic, depending on what file you are reading. Kasper On Jul 20, 2008, at 1:55 PM, Lynn Amon wrote: > Hi Carol, > I've had trouble with read.table also. It doesn't always read all > the rows and columns. I recommend using read.csv(sep="\t") instead. > Lynn Amon > > > Martin Morgan wrote: >> carol white <wht_crl at="" yahoo.com=""> writes: >> >> >>> t >>> = read.table ("my_file", check.names = FALSE, header = >>> T) gives the same result, modifying duplicate >>> names. Carol >> >> what does sessionInfo() say (i.e., is your R current; is this >> something special to your OS or LOCALE)? Have you done this in a >> 'clean' R session, e.g., starting R from the shell with R --vanilla ? >> And for what it's worth >> >> >>> read.table("~/tmp/tmp.txt", header=TRUE, check.names=FALSE) >>> >> AM2 AM2 AM2 FAL >> 1 2 3 4 5 >> 2 1 -1 -3 -2 >> >> >>> sessionInfo() >>> >> R version 2.7.1 Patched (2008-07-03 r46033) x86_64-unknown-linux- gnu >> locale: >> LC_CTYPE >> = >> en_US >> .UTF >> -8 >> ;LC_NUMERIC >> = >> C >> ;LC_TIME >> = >> en_US >> .UTF >> -8 >> ;LC_COLLATE >> = >> en_US >> .UTF >> -8 >> ;LC_MONETARY >> = >> C >> ;LC_MESSAGES >> = >> en_US >> .UTF >> -8 >> ;LC_PAPER >> = >> en_US >> .UTF >> -8 >> ;LC_NAME >> = >> C >> ;LC_ADDRESS >> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics utils datasets grDevices methods >> base Martin >> >> >>> --- On Sat, 7/19/08, Martin Morgan <mtmorgan at="" fhcrc.org=""> >>> wrote >>> : From >>> : Martin Morgan <mtmorgan at="" fhcrc.org=""> Subject: >>> Re: [BioC] problem with read.table To: wht_crl at yahoo.com >>> Cc: bioconductor at stat.math.ethz.ch Date: >>> Saturday, July 19, 2008, 1:52 >>> PM >>> Hi >>> >>> Carol >>> ... Carol >>> white <wht_crl at="" yahoo.com=""> >>> writes >>> : > >>> >>> Hi >>> , > >>> Although I set check.names to FALSE in read.table, the duplicate >>> names >>> get >>> modified >>> . What should be done in this >>> case >>> ? > >>> > >>> the text file to be read by >>> read >>> .table >>> > >>> > >>> AM2 AM2 AM2 >>> FAL >>> > >>> 2 >>> 3 >>> 4 >>> 5 >>> > >>> 1 -1 -3 >>> -2 >>> > >>> > >>> t = read.table ("my_file", check.names = F, header = >>> T >>> ) Maybe >>> spell out TRUE, FALSE (reserved words, cannot be assigned to) >>> to >>> avoid >>> getting the value of variables T, F from your >>> environment >>> ?? Martin >>> > >>> > >>> t >>> > >>> AM2 AM2.1 AM2.2 >>> FAL >>> > >>> > >>> 2 3 >>> 4 >>> 5 >>> > >>> > >>> 1 -1 -3 >>> -2 >>> > >>> > >>> instead >>> of >>> > >>> > >>> AM2 AM2 AM2 >>> FAL >>> > >>> > >>> > >>> 2 3 >>> 4 >>> 5 >>> > >>> > >>> > >>> 1 -1 -3 >>> -2 >>> > >>> > >>> > >>> >>> Best >>> , > >>> >>> carol >>> > >>> > >>> > >>> > >>> > >>> [[alternative HTML version >>> deleted >>> ]] > >>> > >>> >>> _______________________________________________ >>> > >>> Bioconductor mailing >>> list >>> > >>> >>> Bioconductor >>> @stat >>> .math >>> .ethz >>> .ch >>> > >>> https >>> ://stat.ethz.ch/mailman/listinfo/ >>> bioconductor >>> > >>> Search the >>> archives >>> : http >>> ://news.gmane.org/ >>> gmane >>> .science >>> .biology >>> .informatics >>> .conductor >>> -- Martin >>> >>> Morgan >>> Computational >>> Biology / Fred Hutchinson Cancer Research >>> Center >>> 1100 >>> Fairview Ave. >>> N >>> . PO >>> Box 19024 Seattle, WA >>> 98109 >>> Location >>> : Arnold Building M2 >>> B169 >>> Phone >>> : (206) 667-2793 >>> >>> >> >> > > _______________________________________________ > 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