Dear List, I have a time course experiment with three time points and 5 replicates for each time point. I want to get an expression profile from this data, and get the differential expression for different time points. I am new at this so please disregard the trivial nature of this question. How can I analyze this type of data? Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076

This is a 1-way ANOVA and can readily be handled using the limma package in Bioconductor. I suggest that you read through the limma documentation, trying out each example using your own data at each step. If you have Affy data, you will need to normalize the data in Affy first. Otherwise, you can go straight to limma. --Naomi p.s. There must be many people who could help you ad Cold Spring Harbor. At 04:33 PM 12/6/2005, Khan, Sohail wrote: >Dear List, > >I have a time course experiment with three time points and 5 >replicates for each time point. I want to get an expression >profile from this data, and get the differential expression for >different time points. I am new at this so please disregard the >trivial nature of this question. How can I analyze this type of data? > > > > >Sohail Khan >Scientific Programmer >COLD SPRING HARBOR LABORATORY >Genome Research Center >500 Sunnyside Boulevard >Woodbury, NY 11797 >(516)422-4076 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor 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

Dear Sohail, Limma can perform time course analysis. Just have a look at the manual, where there is an example of a time course experiment. Also there is another package called Timecourse, but I think it focuses on analysis of dependent data. Hope this helps, David > Dear List, > > I have a time course experiment with three time points and 5 replicates for each time point. I want to get an expression profile from this data, and get the differential expression for different time points. I am new at this so please disregard the trivial nature of this question. How can I analyze this type of data? > > > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

maSigPro package very easy to use you must first normalized your data (gcrma or whatever) and then...voila!! after playing around it gives you significant genes taking into account time as a variable, good luck! Mensaje citado por "Khan, Sohail" <khan at="" cshl.edu="">: > Dear List, > > I have a time course experiment with three time points and 5 replicates for > each time point. I want to get an expression profile from this data, and > get the differential expression for different time points. I am new at this > so please disregard the trivial nature of this question. How can I analyze > this type of data? > > > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >