-----Messaggio originale----- Da: simonegri at alice.it Inviato: gio 02/08/2007 8.31 A: carol white; Jenny Drnevich; Benjamin Otto; Kauer Maximilian Otto; bioconductor at stat.math.ethz.ch; bioconductor at stat.math.ethz.ch Cc: Bioconductor at stat.math.ethz.ch Oggetto: Two way anova or manova? I have to compare four different grape varieties proteome in two different years. I don't know what test would be more suitable for my data. I think that an anova two way can be usefull also if someone suggested me to perform a manova. In addiction, I can perform each test on a single protein a time, but I can't loose my whole life carrying out anova (I have more than 1000 protein to analyze)!!! I would like to perform the test on every column of the dataframe in a single run. How can I do that? I attach an example of some protein of my dataset ********** Scopri la nuova Alice Mail! 1 GB di spazio con antivirus, antispam e fino a 2 GB di allegati. Registrati GRATIS su http://registra.rossoalice.alice.it/registra/basi c/entratabasic.do?entryPoint=footer ********** Scopri la nuova Alice Mail! 1 GB di spazio con antivirus, antispam e fino a 2 GB di allegati. Registrati GRATIS su http://registra.rossoalice.alice.it/registra/basi c/entratabasic.do?entryPoint=footer

Have a look at limma, samr or MAANOVA. These methods are available for any high-dimensional comparisons, not just microarrays. --Naomi At 02:54 AM 8/2/2007, simonegri at alice.it wrote: >-----Messaggio originale----- >Da: simonegri at alice.it >Inviato: gio 02/08/2007 8.31 >A: carol white; Jenny Drnevich; Benjamin Otto; Kauer Maximilian >Otto; bioconductor at stat.math.ethz.ch; bioconductor at stat.math.ethz.ch >Cc: Bioconductor at stat.math.ethz.ch >Oggetto: Two way anova or manova? > >I have to compare four different grape varieties proteome in two >different years. I don't know what test would be more suitable for >my data. I think that an anova two way can be usefull also if >someone suggested me to perform a manova. In addiction, I can >perform each test on a single protein a time, but I can't loose my >whole life carrying out anova (I have more than 1000 protein to >analyze)!!! I would like to perform the test on every column of the >dataframe in a single run. How can I do that? I attach an example of >some protein of my dataset > > > > > >********** >Scopri la nuova Alice Mail! >1 GB di spazio con antivirus, antispam e fino a 2 GB di allegati. > >Registrati GRATIS su >http://registra.rossoalice.alice.it/registra/basic/entratabasic.do?en tryPoint=footer > > > > > >********** >Scopri la nuova Alice Mail! >1 GB di spazio con antivirus, antispam e fino a 2 GB di allegati. > >Registrati GRATIS su >http://registra.rossoalice.alice.it/registra/basic/entratabasic.do?en tryPoint=footer >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

You can try applying a method named ASCA-genes that is a combination of an ANOVA model for two factors (in your case: grape varieties and years) with a dimension reduction technique to summarizes the main information and identify the genes (proteins) that follow the discovered patterns. The program is in R avaible in http://www.ivia.es/centrogenomica/bioinformatics.htm, and the paper is Nueda, et al. (2007)"Discovering gene expression patterns in Time Course Microarray Experiments by ANOVA-SCA", BIONFORMATICS, May, 22. ----- Original Message ----- From: <simonegri@alice.it> To: <bioconductor at="" stat.math.ethz.ch=""> Sent: Thursday, August 02, 2007 8:54 AM Subject: [BioC] I: Two way anova or manova? -----Messaggio originale----- Da: simonegri at alice.it Inviato: gio 02/08/2007 8.31 A: carol white; Jenny Drnevich; Benjamin Otto; Kauer Maximilian Otto; bioconductor at stat.math.ethz.ch; bioconductor at stat.math.ethz.ch Cc: Bioconductor at stat.math.ethz.ch Oggetto: Two way anova or manova? I have to compare four different grape varieties proteome in two different years. I don't know what test would be more suitable for my data. I think that an anova two way can be usefull also if someone suggested me to perform a manova. In addiction, I can perform each test on a single protein a time, but I can't loose my whole life carrying out anova (I have more than 1000 protein to analyze)!!! I would like to perform the test on every column of the dataframe in a single run. How can I do that? I attach an example of some protein of my dataset ********** Scopri la nuova Alice Mail! 1 GB di spazio con antivirus, antispam e fino a 2 GB di allegati. Registrati GRATIS su http://registra.rossoalice.alice.it/registra/basic/entratabasic.do?ent ryPoint=footer ********** Scopri la nuova Alice Mail! 1 GB di spazio con antivirus, antispam e fino a 2 GB di allegati. Registrati GRATIS su http://registra.rossoalice.alice.it/registra/basic/entratabasic.do?ent ryPoint=footer ---------------------------------------------------------------------- ------ ---- > _______________________________________________ > 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