dat2$genes is probably a data.frame or matrix, not a vector On 28/09/2010, at 12:03 AM, Steve Lianoglou wrote: > Hi, > > On Mon, Sep 27, 2010 at 7:09 AM, Budhayash Gautam > <budhayashgautam at="" gmail.com=""> wrote: >> Dear all >> >> i am working on some smd data which is basically two color data. i >> have normalize the data by the following command >> >> >>> dat2<-normalizeWithinArrays(dat, method="loess","normexp", offset=50) >> >> but as now i am trying to save its expression values by the following >> command its is not giving any genes names with respect to rows without >> which further analysis (annotation etc ) could not be done . >> >>> dat.m<-dat2$M >>> rownames(dat.m)<-dat2$genes$ProbeName >>> write.table(dat.m, "tgondiiexpressionvalues.txt", sep="\t", row.names=T, col.names=T, quote=F) > > This gives you probe id's, right? You can "reverse engineer" which > probes map to which genes using several methods. Depending on the > array you are using, one way would be to query biomart (using the > biomaRt bioc package) for a list of probe id's for your chip and have > it return the probe id & the gene symbol, or entrez id, or whatever > you like. > > Another way would be to use one of the many annotation packages > available from bioconductor. > >>> rownames(dat.m) <-dat2$genes >> >> following error is coming ..... >> >> Error in dimnames(x) <- dn : >> length of 'dimnames' [1] not equal to array extent > > That's because the number of rows in your `dat.m` matrix does not > equal the length of your dat2$genes vector, so R can't make much sense > of the assignment you are trying to make. > > Look at the result of: > > R> nrow(dat.m) == length(dat2$genes) > > Where did you get the dat2$genes vector? Perhaps you can show us what > you get from: > > R> head(dat2$genes) > > is it possible that the probe id's are the names() of this vector? > That could make your life a bit easier. > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > 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