Hi, Suppose this situation: There is a structure in a cell. This one is composed by five proteins. All that is essential. But, in that organism only three are known. If I have the expression for all genes, is it possible to cluster all expression in relation to expression of this three genes? I am looking if any of that genes group together this three. I can do a cluster with all genes, but I would like to cluster one group knowing that another group exist. What you mean about my guess? You known a manner to do this? There is BioConductor package to do this? My normalized data are in a limma MA object. All comments is very appreciated. Thank you very much. -- Marcelo Luiz de Laia Ph.D Candidate S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof. Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Phone: +55-016-3209-2675 Cell: +55-016-97098526

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On Monday 12 February 2007 05:42, Marcelo Laia wrote: > Hi, > > Suppose this situation: > There is a structure in a cell. This one is composed by five > proteins. All that is essential. But, in that organism only three are > known. > > If I have the expression for all genes, is it possible to cluster > all expression in relation to expression of this three genes? > > I am looking if any of that genes group together this three. I can > do a cluster with all genes, but I would like to cluster one group > knowing that another group exist. > > What you mean about my guess? You known a manner to do this? There > is BioConductor package to do this? > > My normalized data are in a limma MA object. It sounds like you want to find genes that are similar in expression pattern to your three known genes. You might look at using a correlation or a distance metric between your known genes and all other genes on your array. The cor() function computes correlation. Sean

Hi I'm not sure what you're looking for here - if you just want to see which other genes correlate to your three of interest, then you could just use the cor() function and a cut-off. If you want to look at the behaviour of groups of genes found by clustering one set of data in a second set of data, then I have published coxpress last year that does exactly that http://coxpress.sf.net Mick ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Marcelo Laia Sent: Mon 12/02/2007 10:42 AM To: Bioconductor Subject: [BioC] cluster a set of genes based on another set of genes Hi, Suppose this situation: There is a structure in a cell. This one is composed by five proteins. All that is essential. But, in that organism only three are known. If I have the expression for all genes, is it possible to cluster all expression in relation to expression of this three genes? I am looking if any of that genes group together this three. I can do a cluster with all genes, but I would like to cluster one group knowing that another group exist. What you mean about my guess? You known a manner to do this? There is BioConductor package to do this? My normalized data are in a limma MA object. All comments is very appreciated. Thank you very much. -- Marcelo Luiz de Laia Ph.D Candidate S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof. Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Phone: +55-016-3209-2675 Cell: +55-016-97098526 _______________________________________________ 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

Hi, You may also want to have a look at: http://bioconductor.org/packages/1.9/bioc/html/geneRecommender.html It might do what you are wanting to do? a > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Marcelo Laia > Sent: 12 February 2007 10:43 > To: Bioconductor > Subject: [BioC] cluster a set of genes based on another set of genes > > > Hi, > > Suppose this situation: > There is a structure in a cell. This one is composed by > five proteins. All that is essential. But, in that organism > only three are known. > > If I have the expression for all genes, is it possible to > cluster all expression in relation to expression of this three genes? > > I am looking if any of that genes group together this > three. I can do a cluster with all genes, but I would like to > cluster one group knowing that another group exist. > > What you mean about my guess? You known a manner to do > this? There is BioConductor package to do this? > > My normalized data are in a limma MA object. > > All comments is very appreciated. > > Thank you very much. > > > -- > Marcelo Luiz de Laia > Ph.D Candidate > S?o Paulo State University (http://www.unesp.br/eng/) > School of Agricultural and Veterinary Sciences > Department of Technology > Via de Acesso Prof. Paulo Donato Castellane s/n > 14884-900 Jaboticabal - SP - Brazil > Phone: +55-016-3209-2675 > Cell: +55-016-97098526 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >