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

> 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\" file1.soft > b.txt"); # 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 > >