Hi Anna, it does not hurt to read the help pages. The function mva.pairs expects a matrix. A call like the following should work: mva.pairs(exprs(eset), log.it=FALSE) (Oddly enough, the default of this function is to log the data.) However, if you have many (n) chips, rather than looking at all n*(n-1)/2 pairs of chips, it might be more illuminating to do something like: A = rowMeans(exprs(eset)) for (i in 1:nrchips) { M = exprs(eset)[,i] - A plot(A, M, pch=".") } Best, Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/mga/whuber ------------------------------------- On Thu, 14 Aug 2003, Anna Gustafsson wrote: > Dear all, > > Unfortunately - more questions: > I wonder how to use mva.pairs to plot 2 replicate slides from an "eset" object of background corrected, normalized, pm corrected and summarized data (i.e rma output). > > I can only find a vignette describing plots from only normalized, non summarized (16 individual expression measures / gene plotted) and I do not understand how to transfer that information to work for my data in the "eset" format..... :( > > With hopes on help! > > // Anna :o) > > ******************************************************************** *********************** > Anna Gustafsson > > Royal Institute of Technology > AlbaNova University Center > Stockholm Center for Physics, Astronomy and Biotechnology > Department of Molecular Biotechnology > 106 91 Stockholm, Sweden > > Phone (office): +46 8 553 783 41 > Fax: + 46 8 553 784 81 > Visiting adress: Roslagstullsbacken 21, Floor 3 > Delivery adress: Roslagsv?gen 30B > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

If you are talking about the RMA background then I have a brief description on this page http://www.stat.berkeley.edu/users/bolstad/ComputeRMAFAQ/ComputeRMAFAQ .html and there are numerous other documents on my website also explaining it. If you are interested in the other "background" methods implemented in the affy package look at the vignette entitled "affy: Built-in Processing Methods" which give a description of each of the methods. You can get the vignettes by typing openVignette() (they are also on the bioconductor website). Ben On Thu, 2003-08-28 at 03:58, Marcus wrote: > Hello all! > > First of all I would like to thank everybody for a great mailing list, it > has halped me a lot. > > Question: How is the background calculated and how is it stored in my > affybatch object? > Is it derived from the mm values or does it originate from other data? > > Best regards > > /Marcus > > > ******************************************************************** *********************** > Marcus Gry Bj?rklund > > Royal Institute of Technology > AlbaNova University Center > Stockholm Center for Physics, Astronomy and Biotechnology > Department of Molecular Biotechnology > 106 91 Stockholm, Sweden > > Phone (office): +46 8 553 783 39 > Fax: + 46 8 553 784 81 > Visiting adress: Roslagstullsbacken 21, Floor 3 > Delivery adress: Roslagsv?gen 30B > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad