Hi, > Date: Mon, 27 Sep 2010 16:39:12 +0530 > From: Budhayash Gautam <budhayashgautam at="" gmail.com=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] how to save the expression values for two color data > after normalization > Message-ID: > <aanlktik0d7ikiungb-dmkuimfur_cxqzhebs0-thjgwk at="" mail.gmail.com=""> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear all > > i am working on some smd data which is basically two color data. i > have normalize the data by the following command > > > > dat2<-normalizeWithinArrays(dat, method="loess","normexp", > > offset=50) > > but as now i am trying to save its expression values by the following > command its is not giving any genes names with respect to rows without > which further analysis (annotation etc ) could not be done . > > > dat.m<-dat2$M > > rownames(dat.m)<-dat2$genes$ProbeName > > write.table(dat.m, "tgondiiexpressionvalues.txt", sep="\t", > > row.names=T, col.names=T, quote=F) > > > and if i am trying ... > > > rownames(dat.m) <-dat2$genes > > > following error is coming ..... > > Error in dimnames(x) <- dn : > length of 'dimnames' [1] not equal to array extent You can export this data in following way: 1. Identify names of your columns, using rownames(dat2$M) and rownames(dat2$A). 2. Next write code like this: data_to_export=cbind(ID=dat$genes$ID *and the rest annotation columns in similar way ,first_array_Mvalue=dat2$M[,1] ,first_array_Avalue=dat2$A[,1] *and so on, numbers in square-brackets corresponds to order of your M and A values) 3. Export to tab-delimited file: write.table(data_to_export,"path/file_name.txt",quote=FALSE,sep="\t") Hope it helps, > > As i am very new to bioconductor and R problem may be very small but > for me it is too big...... > > thus please help me to solve this > > please help me in the creation of proper matrix for the further > analysis. > > > -- > BUDHAYASH GAUTAM > Assistant Professor > Department Of Computational Biology And Bioinformatics, > Jacob School of Biotechnology & Bioengineering (JSBB) > Sam Higginbottom Institute of Agriculture, Technology and Sciences > (SHIATS)- Deemed University, Naini, Allahabad. > U.P. 211007 Maciej Jo?czyk, MSc Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 ___________________________________ NOCC, http://nocc.sourceforge.net