Hi, Today I read a paper in Plant Cell, and the researcheres used GeneSpring 4.2 software (Silicon Genetics, Redwood, CA) to nomalize their data. I wonder if anyone here knows something about the software, and if this software has more function than limma. Thank you very much! -- Xiaopeng ZHANG<xpzhang@genetics.ac.cn>

:-) GeneSpring is a good piece of software for those who can afford it, and is excellent for the production and visualisation of heatmaps and dendrograms. However, I can guarentee you that the Bioconductor microarray packages (and there are many!) have WAY more functionality than any commercial package :-) -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of xpzhang Sent: Thu 11/25/2004 8:44 AM To: bioconductor Cc: Subject: [BioC] Could limma be as good as GeneSpring in nomalization? Hi, Today I read a paper in Plant Cell, and the researcheres used GeneSpring 4.2 software (Silicon Genetics, Redwood, CA) to nomalize their data. I wonder if anyone here knows something about the software, and if this software has more function than limma. Thank you very much! -- Xiaopeng ZHANG<xpzhang@genetics.ac.cn> _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Someone once demonstrated the normalisation procedures in GeneSpring. I think they had MAS 4.0, MAS 5.0 and RMA at the time. However what was interesting is that all of this were (visibly) calling R scripts to BioConductor packages to perform the normalisation. If the trend continues, then I believe their normalisation procedures will be a subset of those available in R/BioConductor. My perception is that people mainly use GeneSpring for graphical purposes and normalisation is seen as "do once and forget about it". Others can correct me if I am wrong in my opinion of GeneSpring and normalisation. Regards, Adai On Thu, 2004-11-25 at 08:44, xpzhang wrote: > Hi, > > Today I read a paper in Plant Cell, and the researcheres used GeneSpring > 4.2 software (Silicon Genetics, Redwood, CA) to nomalize their data. I > wonder if anyone here knows something about the software, and if this > software has more function than limma. > > Thank you very much!