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Hi John The attributes of any good reference sample are that it is constant between experiments and that it lights up the majority of spots. If your genomic DNA meets these criteria, then there is not a problem. I myself have analysed data like this. The main issue is that the genomic DNA reference tends to be much stronger in intensity than the RNA sample, so it is useful to avoid saturation in the reference channel whilst scanning. If the assumption that the majority of genes will not be changing, and that the the average ratio will be 1, is still valid biologically, then the normalisation methods such as median, loess etc are still valid. Once you have a good measure for the relative expression of each gene, limma is a good package to use, and one on which the IAH has standardised on Michael Watson Head of Informatics Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire RG20 7NN UK Phone : +44 (0)1635 578411 ext. 2535 Mobile: +44 (0)7990 827831 E-mail: michael.watson at bbsrc.ac.uk -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of john seers (IFR) Sent: 13 February 2006 15:25 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Genomic DNA as a reference and limma Hello All I have some data using genomic DNA as a reference and I am not quite sure what the implications are of this are. For instance is limma a suitable package to analyse this? Would I have to do something extra with the data? If anybody has any experience of this or can point me to any suitable documentation I would be grateful. Regards John Seers --- John Seers Institute of Food Research Norwich Research Park Colney Norwich NR4 7UA tel +44 (0)1603 251490 fax +44 (0)1603 255167 e-mail john.seers at bbsrc.ac.uk e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ <http: www.ifr.ac.uk="" edisclaimer=""/> www.ifr.ac.uk <http: www.ifr.ac.uk=""/> www.foodandhealthnetwork.com <http: www.foodandhealthnetwork.com=""/> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor