I am comparing gene expression profile in animal model at different time point: Animals Age WT 400 Trans 400 WT 700 Trans 700 WT 800 Trans 800 All experiments are perfomed with 3 biological replicates in each group with Affy chips. I am looking for differentially expressed genes in each groups as well as dynamics of gene profiles in all groups, e.g how genes A......Z are expressed in all groups. What is the best way to analyse this type of experiments and which package is suitable. Thanks in advance Narendra

Hello, You can find in the Bioconductor the maSigPro package which is specially designed for this purpose. After fitting a model for each gene, you can make the queries you look for. Take a look at the maSigPro documentation for details on the use of the package. MAR?A --- Original Message ----- From: "Narendra Kaushik" <kaushiknk@cardiff.ac.uk> To: <bioconductor at="" stat.math.ethz.ch=""> Sent: Monday, October 22, 2007 5:36 PM Subject: [BioC] Time-point analysis > I am comparing gene expression profile in animal model at different time point: > > Animals Age > WT 400 > Trans 400 > WT 700 > Trans 700 > WT 800 > Trans 800 > > All experiments are perfomed with 3 biological replicates in each group with Affy chips. I am > looking for differentially expressed genes in each groups as well as dynamics of gene profiles in > all groups, e.g how genes A......Z are expressed in all groups. > What is the best way to analyse this type of experiments and which package is suitable. > > Thanks in advance > > Narendra > > _______________________________________________ > 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

In addition to the packages specifically designed for time course experiments, the linear modelling approach of the limma package applies nicely to the time course problem. See the section of time course experiments in the limma User's Guide. Gordon >Message: 12 >Date: Mon, 22 Oct 2007 18:52:26 +0200 >From: M? Jos? Nueda <mj.nueda at="" ua.es=""> >Subject: Re: [BioC] Time-point analysis >To: "Narendra Kaushik" <kaushiknk at="" cardiff.ac.uk=""> >Cc: bioconductor at stat.math.ethz.ch >Message-ID: <016e01c814cb$ed22da20$456e10ac at MJN> >Content-Type: text/plain; charset="iso-8859-1" > >Hello, > >You can find in the Bioconductor the maSigPro package which is specially >designed for this purpose. >After fitting a model for each gene, you can make the queries you look for. >Take a look at the maSigPro documentation for details on the use of the >package. > >MAR?A > >--- Original Message ----- >From: "Narendra Kaushik" <kaushiknk at="" cardiff.ac.uk=""> >To: <bioconductor at="" stat.math.ethz.ch=""> >Sent: Monday, October 22, 2007 5:36 PM >Subject: [BioC] Time-point analysis > > > > I am comparing gene expression profile in animal model at different time >point: > > > > Animals Age > > WT 400 > > Trans 400 > > WT 700 > > Trans 700 > > WT 800 > > Trans 800 > > > > All experiments are perfomed with 3 biological replicates in each group >with Affy chips. I am > > looking for differentially expressed genes in each groups as well as >dynamics of gene profiles in > > all groups, e.g how genes A......Z are expressed in all groups. > > What is the best way to analyse this type of experiments and which package >is suitable. > > > > Thanks in advance > > > > Narendra