Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the directory of these .cel files. I don't know how to give the path for all these files. i set the path as given below,> rna.data<-exprs(justRMA(filenames=file.names, celfile.path="*D:/MONO1.CEL""D:/MONO2.CEL" "D:/MONO3.CEL" "D:/MACRO1.CEL" "D:/MACRO2.CEL" "D:/MACRO3.CEL"*,sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) it shows this error, Error: unexpected string constant in "rna.data<-exprs(justRMA(filenames=file.names, celfile.path="D:/MONO1" "D:/MONO2"" could u please help me in this case. Thanks in advance. with regards, S.Mahalakshmi [[alternative HTML version deleted]]
Dear Mahalakshmi, the simplest way to do this and to avoid your error is to open R directtly for the folder in which there are your .CEL files and then: data<-ReadAffy() #read all the .CEL files in the working director data.rma<-rma(data) #in order to use rma on your .CEL files hope helps 2010/3/4 mahalakshmi sivamani <mahasiva1987 at gmail.com>:> Hi all , > > I have one query. > > i have list of some ?.cel files. in my program i have to mention the path of > these .cel files > > part of my program is, > > rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, > sampleNames=sample.names, phenoData=pheno.data, > cdfname=cleancdfname(hg18_Affymetrix U133A))) > > > in the place of "datadir" i have to mention the character string of the > directory of these .cel files. I don't know how to give the path for all > these files. > > i set the path as given below, > > >> rna.data<-exprs(justRMA(filenames=file.names, celfile.path="*D:/MONO1.CEL" > "D:/MONO2.CEL" "D:/MONO3.CEL" "D:/MACRO1.CEL" "D:/MACRO2.CEL" > "D:/MACRO3.CEL"*,sampleNames=sample.names, phenoData=pheno.data, > cdfname=cleancdfname(hg18_Affymetrix U133A))) > > > it shows this error, > > Error: unexpected string constant in > "rna.data<-exprs(justRMA(filenames=file.names, celfile.path="D:/MONO1" > "D:/MONO2"" > > > could u please help me in this case. > > > Thanks in advance. > > > with regards, > > S.Mahalakshmi > > ? ? ? ?[[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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. >-- ----------------------------------------------------- Dr. Alberto Goldoni Bologna, Italy
On 03/04/2010 10:30 PM, mahalakshmi sivamani wrote:> Hi all , > > I have one query. > > i have list of some .cel files. in my program i have to mention the path of > these .cel files > > part of my program is, > > rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, > sampleNames=sample.names, phenoData=pheno.data, > cdfname=cleancdfname(hg18_Affymetrix U133A))) > > > in the place of "datadir" i have to mention the character string of the > directory of these .cel files. I don't know how to give the path for all > these files. > > i set the path as given below, > > >> rna.data<-exprs(justRMA(filenames=file.names, celfile.path="*D:/MONO1.CEL" > "D:/MONO2.CEL" "D:/MONO3.CEL" "D:/MACRO1.CEL" "D:/MACRO2.CEL" > "D:/MACRO3.CEL"*,sampleNames=sample.names, phenoData=pheno.data, > cdfname=cleancdfname(hg18_Affymetrix U133A))) > > > it shows this error, > > Error: unexpected string constant in > "rna.data<-exprs(justRMA(filenames=file.names, celfile.path="D:/MONO1" > "D:/MONO2"" > >Hi Mahalakshmi, If you want to pass more than one string as an argument, you must pass them as a character vector. celfile.path=c("D:/MONO1.CEL","D:/MONO2.CEL","D:/MONO3.CEL", "D:/MACRO1.CEL","D:/MACRO2.CEL","D:/MACRO3.CEL") Although this is not guaranteed to make your function work correctly. Jim
Hello All, I am new to R and tried to install R in Linux system (OS: Open SUSE). After untar the source code, changed the directory, and typed the command ./configure, it was checking a list...finally it gave an error message. Here with i have enclosed the error message. Check-list goes like this: checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/i586-suse-linux/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/i586-suse-linux/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... no checking readline/history.h presence... no checking for readline/history.h... no checking readline/readline.h usability... no checking readline/readline.h presence... no checking for readline/readline.h... no checking for rl_callback_read_char in -lreadline... no checking for main in -lncurses... yes checking for rl_callback_read_char in -lreadline... no checking for history_truncate_file... no configure: error: --with-readline=yes (default) and headers/libs are not available Can anyone help me in this regard? Expecting your reply and thanks in advance. Warm regards Fredrick.
Hi Fredrick, Is there a reason you need to compile the source code? If not, I recommend following the instillation instructions on CRAN. OpenSuse instructions are at http://cran.r-project.org/bin/linux/suse/ Best, Ista On Tue, Mar 23, 2010 at 7:43 AM, fredrick devadoss <fredrick_isro at yahoo.com> wrote:> Hello All, > > I am new to R and tried to install R in Linux system (OS: Open SUSE). > After untar the source code, changed the directory, and typed the > command ./configure, it was checking a list...finally it gave an error > message. Here with i have enclosed the error message. > > Check-list goes like this: > > checking if g++ supports -c -o file.o... yes > checking if g++ supports -c -o file.o... (cached) yes > checking whether the g++ linker (/usr/i586-suse-linux/bin/ld) supports shared libraries... yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... no > checking for gfortran option to produce PIC... -fPIC > checking if gfortran PIC flag -fPIC works... yes > checking if gfortran static flag -static works... yes > checking if gfortran supports -c -o file.o... yes > checking if gfortran supports -c -o file.o... (cached) yes > checking whether the gfortran linker (/usr/i586-suse-linux/bin/ld) supports shared libraries... yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > checking for cos in -lm... yes > checking for sin in -lm... yes > checking for dlopen in -ldl... yes > checking readline/history.h usability... no > checking readline/history.h presence... no > checking for readline/history.h... no > checking readline/readline.h usability... no > checking readline/readline.h presence... no > checking for readline/readline.h... no > checking for rl_callback_read_char in -lreadline... no > checking for main in -lncurses... yes > checking for rl_callback_read_char in -lreadline... no > checking for history_truncate_file... no > configure: error: --with-readline=yes (default) and headers/libs are not available > > Can anyone help me in this regard? > > Expecting your reply and thanks in advance. > > Warm regards > Fredrick. > > ______________________________________________ > R-help at 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. >-- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org
Hello, I would like to create all combinations of vectors. I find on Matalb this function 'combvec' which create all combinations of vectors. Please could you help me to find the corresponds function of 'combvec'. For example: On Matlab>> a1 = [1 2 3; 4 5 6]a1 1 2 3 4 5 6>> a2 = [7 8; 9 10]a2 7 8 9 10>> a3 = combvec(a1,a2)a3 1 2 3 1 2 3 4 5 6 4 5 6 7 7 7 8 8 8 9 9 9 10 10 10 Best Regards [[alternative HTML version deleted]]
Hi, Thank you for your help. this function 'combvec ' takes any number of inputs on Matlab. So, you can take more than two matrix. The help of this function 'combvec' is like this on Matlab:>> help combvecCOMBVEC Create all combinations of vectors. Syntax combvec(a1,a2,...) Description COMBVEC(A1,A2,...) takes any number of inputs, A1 - Matrix of N1 (column) vectors. A2 - Matrix of N2 (column) vectors. and returns a matrix of (N1*N2*...) column vectors, where the columns consist of all possibilities of A2 vectors, appended to A1 vectors, etc. Example a1 = [1 2 3; 4 5 6]; a2 = [7 8; 9 10]; a3 = combvec(a1,a2) 2010/4/19 Dennis Murphy <djmuser@gmail.com>> Hi: > > This is a simplistic version of combvec that works for two input matrices; > I don't > have Matlab, and I don't understand how the function generalizes to more > than > two input matrices, so this is the best I can offer, for what it's worth... > > combvec2 <- function(m1, m2) { > c1 <- ncol(m1) > c2 <- ncol(m2) > k1 <- kronecker(matrix(rep(1, c2), nrow = 1), m1) > k2 <- kronecker(m2, matrix(rep(1, c1), nrow = 1)) > rbind(k1, k2) > } > > > a1 <- matrix(1:6, nrow = 2, byrow = TRUE) > > a1 > [,1] [,2] [,3] > [1,] 1 2 3 > [2,] 4 5 6 > > a2 <- matrix(7:10, nrow = 2, byrow = TRUE) > > > combvec2(a1, a2) > [,1] [,2] [,3] [,4] [,5] [,6] > [1,] 1 2 3 1 2 3 > [2,] 4 5 6 4 5 6 > [3,] 7 7 7 8 8 8 > [4,] 9 9 9 10 10 10 > > HTH, > Dennis > > On Sun, Apr 18, 2010 at 3:00 AM, anderson nuel <anderson.nue@gmail.com>wrote: > >> Hello, >> >> I would like to create all combinations of vectors. I find on Matalb >> this >> function 'combvec' which create all combinations of vectors. >> >> Please could you help me to find the corresponds function of 'combvec'. >> >> For example: >> >> On Matlab >> >> >> a1 = [1 2 3; 4 5 6] >> >> a1 >> >> 1 2 3 >> 4 5 6 >> >> >> a2 = [7 8; 9 10] >> >> a2 >> >> 7 8 >> 9 10 >> >> >> a3 = combvec(a1,a2) >> >> a3 >> >> 1 2 3 1 2 3 >> 4 5 6 4 5 6 >> 7 7 7 8 8 8 >> 9 9 9 10 10 10 >> >> Best Regards >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> 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. >> > >[[alternative HTML version deleted]]