HI, I'm a student who begin to use R Language, I would like to know how to use genefinder (in library genefilter) in order to search a pattern. In fact, is it possible to assemble all values on the same rank. For example, I have 4 conditions and I search a specific profile. The problem is the genes have differents intensities but they have close pattern of the query. ex: 3 genes A,B,C 4 conditons A(values): 30, 40, 50, 60 B : 100, 110, 120, 130 C : 35, 50, 55, 65 I search the gene with the same gene A profile, genefinder found gene C if I limit numResults = 1. So, I would like to know if it's possible to superimpose on the gene A profile and extract gene B. I played with genescale unsuccessful. Can you help! Thanks, Catherine ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

On Thu, Jun 12, 2003 at 04:12:57PM +0200, Catherine.Eng@stud.unibas.ch wrote: > HI, > > I'm a student who begin to use R Language, I would like to know how to use > genefinder (in library genefilter) in order to search a pattern. In fact, is it > possible to assemble all values on the same rank. > For example, I have 4 conditions and I search a specific profile. The problem > is the genes have differents intensities but they have close pattern of the > query. > > ex: 3 genes A,B,C > 4 conditons > A(values): 30, 40, 50, 60 > B : 100, 110, 120, 130 > C : 35, 50, 55, 65 > You have to choose an appropriate distance metric (by default it is Euclidean) in this case you could either standardize across samples (be careful that this makes sense) or use a correlation base distances. Most of this stuff (including heatmaps,clustering and classification) depends on an appropriate metric Robert > I search the gene with the same gene A profile, genefinder found gene C if I > limit numResults = 1. > So, I would like to know if it's possible to superimpose on the gene A profile > and extract gene B. I played with genescale unsuccessful. > > Can you help! > > Thanks, > > Catherine > > ------------------------------------------------- > This mail sent through IMP: http://horde.org/imp/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+