I am new to bioconductor, so please excuse me if my questions are a faq somewhere...:) I am working on a set of affymetrix chips that I want to do vsn on. Now, I have external ways of examining the results from this, but this is dependent on me being able to map the results from vsn. I am working on the probe level, so in other cases, where the results have been an affybatc, my solution to accessing the data has been to use the command probes(abatch) to get a probe by probe listing of all the intensities. Now, the results from vsn is an exprset, and I cannot find any such information associated with these objects. I am able to utilise not only the probe name, but also the x and y positions on the chips too, but I cannot find a way to associate intensities in the exprset object to such information. Could any of you give me any pointers to what I can do to work around this problem? Thanks! Karin -- Karin Lagesen, PhD student karin.lagesen at medisin.uio.no http://folk.uio.no/karinlag

Dear Karin, you can access the expression data in an exprSet with the "exprs" function, and if the data matrix that went into vsn had row names, the resulting matrix exprs(vsnres) should have rownames, too. Please let me know if this is not the case. Also the dimensions of that output matrix are the same as that of the input matrix and rows and columns remain aligned. On the long run, consider using "vsn2" or "vsnMatrix" from the development branch / release 2.0. The internal algorithm is the same, but the user interface is cleaner, and in addition you now have the possibility to normalize "against" an existing reference fit. Does this help? Best wishes Wolfgang > I am new to bioconductor, so please excuse me if my questions are a > faq somewhere...:) > > I am working on a set of affymetrix chips that I want to do vsn on. > Now, I have external ways of examining the results from this, but this > is dependent on me being able to map the results from vsn. I am > working on the probe level, so in other cases, where the results have > been an affybatc, my solution to accessing the data has been to use > the command probes(abatch) to get a probe by probe listing of all the > intensities. > > Now, the results from vsn is an exprset, and I cannot find any such > information associated with these objects. I am able to utilise not > only the probe name, but also the x and y positions on the chips too, > but I cannot find a way to associate intensities in the exprset object > to such information. > > Could any of you give me any pointers to what I can do to work around > this problem? > > Thanks! > > Karin