On Mon, May 3, 2010 at 8:39 AM, varpal singh <gilvarpal@gmail.com> wrote: > Respected Sir, > > I'm varpal singh, I'm writting to express my interest in clustering. > According your suggestio I got some good results with bioconductor. Now I > have got 847 genes after criteria (P value 0.05 and fold change -1><1 ) > within wild type and mutant each have two replicate. > > I have some problem like: > > Can we do Clustering on the basis of expression value always ? > how can we decide which coefficent is perfect (coef =1 or ceof=2) ? > Plz find out attachment in which some screen shot of my results... (in > which up - down - and both genes clustered separetly..) > But I cant see clearly name of genes on the cluster, plz tell me how can > see ?? > For visualizing 847 gene names, you should consider using a cluster viewer like java treeview. You can use the ctc package to export in a format that treeview understands. And R-only alternative is to make the plots as large pdf files using the pdf() device and specifying a very large height. Sean [[alternative HTML version deleted]]

Respected Sir, I'm varpal singh, I'm writting to express my interest in clustering. According your suggestio I got some good results with bioconductor. Now I have got 847 genes after criteria (P value 0.05 and fold change -1><1 ) within wild type and mutant each have two replicate. I have some problem like: Can we do Clustering on the basis of expression value always ? how can we decide which coefficent is perfect (coef =1 or ceof=2) ? Plz find out attachment in which some screen shot of my results... (in which up - down - and both genes clustered separetly..) But I cant see clearly name of genes on the cluster, plz tell me how can see ?? Thanking you Varpal -------------- next part -------------- A non-text attachment was scrubbed... Name: both.png Type: image/png Size: 46503 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100503="" d053a1cb="" attachment.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: up.png Type: image/png Size: 49570 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100503="" d053a1cb="" attachment-0001.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: dow.png Type: image/png Size: 49610 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100503="" d053a1cb="" attachment-0002.png="">