Dear All, I have data from illumina experiments (one colora data) (48803 rows, 120 colones (40 colones for each treatment) ) and I am looking for the genes differentially expressed by treatment could you tell me please, if i can use the package limma to apply the differential expression methods (lmFit,eBayes and topGene) or other method appropriate to my data ( for instance ANOVA)? Best regards ML [[alternative HTML version deleted]]

On Tue, Mar 24, 2009 at 7:06 PM, Mohamed lajnef <lajnef@gmail.com> wrote: > Dear All, > > I have data from illumina experiments (one colora data) (48803 rows, 120 > colones (40 colones for each treatment) ) and I am looking for the genes > differentially expressed by treatment > > could you tell me please, if i can use the package limma to apply the > differential expression methods (lmFit,eBayes and topGene) or other method > appropriate to my data ( for instance ANOVA)? > Yes. You might want to look at the lumi or beadarray packages, as well. Sean [[alternative HTML version deleted]]

On Wed, Mar 25, 2009 at 4:07 AM, Mohamed lajnef <lajnef@gmail.com> wrote: > Hi Sean & Wei > > I forgot to tell you that the database is normalized using beadarray > package, but i am looking for an appropriate methode (limma,anova or...???) > to extract the genes differentially expressed by treatment > Limma is a fine choice, yes. The limma user guide and help pages are the place to start. Sean > > Mohamed > > 2009/3/25 Sean Davis <seandavi@gmail.com> > >> >> >> On Tue, Mar 24, 2009 at 7:06 PM, Mohamed lajnef <lajnef@gmail.com> wrote: >> >>> Dear All, >>> >>> I have data from illumina experiments (one colora data) (48803 rows, 120 >>> colones (40 colones for each treatment) ) and I am looking for the genes >>> differentially expressed by treatment >>> >>> could you tell me please, if i can use the package limma to apply the >>> differential expression methods (lmFit,eBayes and topGene) or other >>> method >>> appropriate to my data ( for instance ANOVA)? >>> >> >> Yes. You might want to look at the lumi or beadarray packages, as well. >> >> Sean >> >> >> > [[alternative HTML version deleted]]

Hi Mohamed: You have to normalize your data before you use lmFit and eBayes. Cheers, Wei Mohamed lajnef wrote: > Dear All, > > I have data from illumina experiments (one colora data) (48803 rows, 120 > colones (40 colones for each treatment) ) and I am looking for the genes > differentially expressed by treatment > > could you tell me please, if i can use the package limma to apply the > differential expression methods (lmFit,eBayes and topGene) or other method > appropriate to my data ( for instance ANOVA)? > > > Best regards > > ML > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >