thanks, I'm interested in Cox regression type analysis on one side !!! On 01/15/2010 04:38 PM, Claus Mayer wrote: > Hi David! > > I haven't had many data sets like that but as far as I can see limma is not > only capable of comparing groups but you can also have continuous > measurements as explanatory variables, i.e. fit a multiple regression type > of model by defining the design as > > Design<- model.matrix(~ var1 + var2 +..+ varn), > > where var1-varn are n clinical variables. The question is, whether that is > the type of analysis you have in mind. You say "correlate" in your e-mail. > Correlation treats gene expression and clinical variable as equal, whereas > in regression you choose one of them as explanatory the other one as > response. The model above has gene expression as response (separately for > each gene). It is very well possible though that you rather want to explain > the clinical variables by the gene expression profile, i.e reverse the > roles. Limma wouldn't be the right tool for that. Or perhaps one of your > variables is survival time and you want to conduct a cox regression type of > analsyis... etc.. > > I think your message contains too little information to direct you to the > right tool, but if it is indeed a multiple regression you looking for, you > could still use limma (see above). > > Claus > >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- >> bounces at stat.math.ethz.ch] On Behalf Of David martin >> Sent: 15 January 2010 10:47 >> To: bioconductor at stat.math.ethz.ch >> Subject: [BioC] Package on clinical data analysis >> >> Hi, >> I would like to know if there is a package to analyse gene expression >> and correlate with a clinical variable ? >> >> Limma does all sort of gene expression analysis but is there any package >> to correlate that with clinical variables ? >> >> thanks, >> david >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 >