Hi, member[2] - member[3] is going to give an error os the binary operator "-" cannot operate on strings, > member[2] - member[3] Error in member[2] - member[3] : non-numeric argument to binary operator try, design <- diag(3)[rep(1:3, each=2),] colnames(design) <- member member <- LETTERS[1:3] difference <- paste(member[2],"-",member[3], sep="") makeContrasts(difference,levels=design) Marcus On 8/2/06 7:00 PM, "Jay Shin" <jay.shin at="" pharma.ethz.ch=""> wrote: > Hello, > I am trying to run a makeConstrasts() function to compute eBayes t- > test with the following design list (six hybridizations and three > samples -in duplicates): > A B C > 1 1 0 0 > 2 1 0 0 > 3 0 1 0 > 4 0 1 0 > 5 0 0 1 > 6 0 0 1 > > I would like to compare sample "B-C", so when I run: >> contrasts.matrix<-makeContrasts(B-C, levels=design) > it works great! > > However, I have B and C stored in 'member' (e.g. member[1] = B, member > [2] = C). > So, when I try to run: >> member1<-member[1] >> member2<-member[2] >> contrasts.matrix<-makeContrasts(member1-member2, levels=design) > > I get a following error message: > Error in eval(expr, envir, enclos) : object "member1" not found > > Can you please help me how I can directly compare the content of the > 'member' in makeContrasts() function? > Thank you, > Jay > > On Aug 2, 2006, at 4:40 AM, Gordon Smyth wrote: > >> Dear Bjoern, >> >>> Date: Mon, 31 Jul 2006 12:43:00 +0200 >>> From: Bj?rn Usadel <usadel at="" mpimp-golm.mpg.de=""> >>> Subject: [BioC] limma: read.maimages possibility to warn the user? >>> To: bioconductor at stat.math.ethz.ch >>> >>> Dear list, >>> >>> when using read.maimages from limma with a "broken" file (tabs >>> replaced >>> by ":", two extra tabs added at the end of row e) >>> limma reads the table fine >>> >>> table: >>> :R:G:RB:GB >>> a:1:2:0.5:0.5 >>> b:2:4:1:1 >>> c:3:6:1.5:1.5 >>> d:4:8:2:2 >>> e:5:10:2.5:2.5:: >>> f:6:12:3:3 >>> g:7:14:3.5:3.5 >>> >>> code: >>> RG<-read.maimages(files="test.txt", path="C://cpan//",columns=list >>> (Gf="G", >>> Rf="R", >>> Gb="GB", >>> Rb="RB" >>> )) >>> >>> But I get NA values added in all columns thus changing the order of >>> probes in this particular arrayfile >>> $G >>> test >>> [1,] 2 >>> [2,] 4 >>> [3,] 6 >>> [4,] 8 >>> [5,] 10 >>> [6,] NA <- >>> [7,] 12 >>> [8,] 14 >> >> This unfortunate behaviour is due to (what I believe to be) a bug in >> the R function read.table. (I've sent a post to R-devel today to >> discuss it.) You can prevent it simply by adding the argument >> flush=TRUE to your read.maimages() call. This will result in the >> spurious delimiters at the of the end of the lines being ignored. >> >> Perhaps I will add flush=TRUE to the limma read by default. >> >>> Marray on the other hand, complains using the following syntax and >>> refuses to read in the offending file. >>> RG2<-read.marrayRaw(fnames="test.txt",path="C://cpan//", name.Gf="G", >>> name.Rf="R", >>> name.Gb="GB", >>> name.Rb="RB" >>> ) >>> >>> "Error in scan(file = file, what = what, sep = sep, quote = quote, >>> dec = >>> dec, : line 5 did not have 5 elements" >> >> This is something of an accident. If there had been five extra tab >> characters at the end of the line instead of two, then marray would >> have done exactly the same as limma. The difference between the two >> packages is that limma is using fill=TRUE in the read while marray is >> not. This allows limma to read incomplete lines. >> >> Best wishes >> Gordon >> >>> Even though I appreciate, that limma reads the data fine without the >>> usual read.table hazzle and realize that the data should have been >>> checked before reading it in anyway, I think at least a little >>> warning >>> could greatly help. >>> But maybe I missed something important (not being a two color type >>> anyway)? >>> >>> (The broken files result from an MS Excel export and this happens on >>> R2.2 with limma 2.4.13 and on R 2.3.1 with limma 2.6.2) >>> >>> >>> Cheers, >>> Bj?rn >>> >>> >>> -- >>> -+-+-+-+-+-+-+-+-+-+-+- >>> Bj?rn Usadel, PhD >>> >>> Max Planck Institute of Molecular Plant Physiology >>> System Regulation Group >>> >>> Am M?hlenberg 1 >>> D-14476 Golm >>> Germany >>> >>> Tel (+49 331) 567-8114 >>> >>> Email usadel at mpimp-golm.mpg.de >>> WWW mapman.mpimp-golm.mpg.de >> >> _______________________________________________ >> 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 > > ________________________________________________________ > ETH Zurich > Jay W. Shin > Institute of Pharmaceutical Sciences > HCI H394 > Wolfgang-Paulistrasse 10 > 8093 Zurich, Switzerland > > jay.shin at pharma.ethz.ch > www.pharma.ethz.ch > > ++41 44 633 73 68 phone > ++41 44 633 13 64 fax > > > > [[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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}