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Question: Re: Fw: problem with GEO parser
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gravatar for Saurin D. Jani
12.6 years ago by
Saurin D. Jani360 wrote:
I forgot to tell you that this works only for 1 soft file in current dirctory. you can have your softfile in current directory , turn on your R session and cut and paste below parser code..! It will work because I just ran on my computer 2 mins. back and it works fine. you have : GDS461.soft on this soft file, > eset Expression Set (exprSet) with 12625 genes 10 samples phenoData object with 0 variables and 0 cases varLabels -----------cut starts here----------- #-- reading soft file softFile <- list.files(,"soft"); # from local directory system("cp *.soft file1.soft"); system("grep -on \"ID_REF\" file1.soft > b.txt" ); system("grep \"dataset_platform\" file1.soft > d.txt"); ln <- as.matrix(readLines("b.txt")); lm <- as.matrix(readLines("d.txt")); system("rm b.txt"); system("rm d.txt"); system("rm file1.soft"); lnX <- as.matrix(unlist(strsplit(ln[2],":"))) Skpnum <- as.numeric(lnX[1]); lmX <- as.matrix(unlist(strsplit(lm[1],"="))) chiptype <- trimWhiteSpace(lmX[2]); GDSN <- softFile; emX <- read.table(softFile,skip = Skpnum,comment.char = ""); Colm <- ncol(emX); Rnames <- as.matrix(emX["V1"]); temp_emX <- emX; temp2 <- temp_emX[3:Colm]; temp2 <- as.matrix(temp2); rownames(temp2) <- Rnames; #--making expressiong set out of soft file, #soft file has normalized data,so I am assuming here #that this data is also normalized esetX <- as.matrix(temp2); eset <- new("exprSet", exprs = esetX); -----------cut ends here----------- now paste in to your R session. Saurin -- |------------------------------------------------ | Saurin Jani,MS | Statistical and Research Analyst | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29407 (US) | | Email: jani@musc.edu | Phone: (843)792-5483 |------------------------------------------------ Quoting guillaume deplaine <guillaume.deplaine@neuf.fr>: > Hello, > > In april I wrote you a message about my problem with your GEO parser. It's > extremly important for me to open et cluster this file in R. I don't know > why it's the problem with your program. > Could you help me please. > Thanks a lot > ----- Original Message ----- > From: "guillaume deplaine" <guillaume.deplaine@neuf.fr> > To: "Saurin D. Jani" <jani@musc.edu> > Sent: Friday, April 01, 2005 1:33 PM > Subject: problem with GEO parser > > > > Dear colleague, > > > > You sent me a GEO parser you wrote some time ago. > > I have a problem because when I run R, I can read soft file with the > > command > > line softFile<-list.files(,"GDS461.soft"). But after, with the command : > > system("cp *.soft file1.soft") or with system(grep-on\"ID_REF\" file1.soft > > > > > > b.txt"), R console said : cp (or grep) was not found. > > > > You wrote #put your GEO file but I don't know where GDS461.soft must be > > written. > > Perhaps it's a problem of version. I work with R 2.0.1 or I forget a space > > in a command line. > > I enclose GDS461.soft file to my message. > > > > Could you explain me the problem and where, in your script, GDS461.soft > > must > > be written. > > Thanks for your help. > > > > > > Guillaume Deplaine > > > > INSERM U36 > > Coll?ge de France > > 11, place Marcellin Berthelot > > 75231 Paris Cedex 05 > > > > T?l. : 01 44 27 16 54 > > Fax. : 01 44 27 16 91 > > Portable : 06 19 94 82 77 > > E-mail : guillaume.deplaine@neuf.fr > > ----- Original Message ----- > > From: "Saurin D. Jani" <jani@musc.edu> > > To: "Guillaume Deplaine" <guillaume.deplaine@college-de-france.fr> > > Cc: <bioconductor@stat.math.ethz.ch> > > Sent: Tuesday, March 29, 2005 4:18 PM > > Subject: Re: [BioC] problem with GEO site > > > > > >>> I was wishering if it's passible to do a clustering > >>> analysis of this file with R ? > >> > >> you need to parse this file and make expression set in R. for that you > >> need GEO > >> parser and below is GEO parser that I wrote some time ago. > >> > >> ##================================================================ > >> ## GEO SOFT FILES > >> ##================================================================ > >> # GEO soft file parser(1.0) - Saurin Jani > >> > >> #-- reading soft file > >> > >> softFile <- list.files(,"soft"); # from local directory > >> > >> system("cp *.soft file1.soft"); > >> system("grep -on \"ID_REF\"; > >> # put your GEO soft file , b.txt file will be created on your computer > >> > >> system("grep \"dataset_platform\" file1.soft > d.txt"); > >> ln <- as.matrix(readLines("b.txt")); > >> lm <- as.matrix(readLines("d.txt")); > >> > >> system("rm b.txt"); > >> system("rm d.txt"); > >> system("rm file1.soft"); > >> > >> lnX <- as.matrix(unlist(strsplit(ln[2],":"))) > >> Skpnum <- as.numeric(lnX[1]); > >> > >> lmX <- as.matrix(unlist(strsplit(lm[1],"="))) > >> chiptype <- trimWhiteSpace(lmX[2]); > >> GDSN <- softFile; > >> > >> emX <- read.table(softFile,skip = Skpnum,comment.char = ""); > >> Colm <- ncol(emX); > >> > >> Rnames <- as.matrix(emX["V1"]); > >> temp_emX <- emX; > >> > >> temp2 <- temp_emX[3:Colm]; > >> temp2 <- as.matrix(temp2); > >> rownames(temp2) <- Rnames; > >> > >> #--making expressiong set out of soft file, soft file has normalized > >> data,so I am > >> #---assuming here that this data is also normalized > >> > >> esetX <- as.matrix(temp2); > >> eset <- new("exprSet", exprs = esetX); > >> > >> > >> you can use eset for clustering. > >> > >> > >> Saurin > >> -- > >> |------------------------------------------------ > >> | Saurin Jani,MS > >> | Statistical and Research Analyst > >> | > >> | Department of Cell Biology and Anatomy > >> | Medical University of South Carolina (MUSC) > >> | 173 Ashley Ave > >> | Charleston,SC - 29407 (US) > >> | > >> | Email: jani@musc.edu > >> | Phone: (843)792-5483 > >> |------------------------------------------------ > >> > >> > >> Quoting Guillaume Deplaine <guillaume.deplaine@college-de- france.fr="">: > >> > >>> Hello, > >>> > >>> I found a file on GEO web site. this files was processed with MASS 4 > >>> until normalization. I was wishering if it's passible to do a clustering > >>> analysis of this file with R ? > >>> > >>> My second question is if it's possible to retrieve raw data of this > >>> file > >>> > >>> processed with MASS 4? > >>> > >>> Thanks for your answer > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> > >>> > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
ADD COMMENTlink written 12.6 years ago by Saurin D. Jani360
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