Hi all, I would recommend the Probe Profile rather than the Gene Profile. If you look at the number of rows in each, you will see that the Gene Profile has less rows meaning that it has averaged over the probes which map to the same gene. We often see that the probes matching to the same gene have inconsistent values so averaging in this way is not ideal. Hope this helps, Mark On 8 Aug 2007, at 10:22, Cei Abreu-Goodger wrote: > I was asking about it in a previous email... Probe Profile data gets > slightly messed up with the "lumiMouseV1" package, so I would suggest > sticking to Gene Profile data, for now... > > Cei > > Yogi Sundaravadanam wrote: >> Hi all >> >> >> >> Is it better to use Probe Profile or Gene Profile for illumine >> analysis >> or it doesn?t matter? I have been using Gene_Profile.csv for >> analysis >> and it seems OK. >> >> >> >> Any thoughts would be greatly appreicated. >> >> Yogi >> >> >> >> _____ >> >> Yoganand Sundaravadanam >> Bioinformatics Officer >> >> Australian Genome Research Facility Ltd >> Level 5 Gehrmann Laboratories >> Research Road >> University of Queensland >> St Lucia QLD >> Phone: +61 7 3346 7328 >> Fax: +61 7 3365 1823 >> >> Email: yogi.sundaravadanam at agrf.org.au >> Web: www.agrf.org.au >> Subscribe to the AGRF Newsletter >> >> _____ >> >> Please Note: The message is intended only for the addressee. If you >> receive this message in error please do not publish, distribute, >> or copy >> it. Please advise the AGRF by telephone or email, and delete this >> message from your computer. >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> --------------------------------------------------------------------- >> --- >> >> _______________________________________________ >> 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 > > > -- > Cei Abreu-Goodger, PhD > > Wellcome Trust Sanger Institute > Computational and Functional Genomics > Wellcome Trust Genome Campus > Hinxton, Cambridge, CB10 1SA, UK > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > _______________________________________________ > 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