Hello All I'm having difficulties carrying out a time series analysis of my dataset using Bioconductor! Could anyone help me out in this area: I have microarray time course data for 1hr, 2hr, 3hr and 4hr time points: Treatment E1H1 E1H2 =A E1H3 E2H1 E2H2 =B E2H3 E3H1 E3H2 =C E3H3 E4H1 E4H2 =D E4H3 pooled Control dataset R1H1 R2H2 R3H3 =E R4H4 the design matrix is such that I compared each total replicate in the treatment i.e A, B, C, and D with E. Thus A is compared with E B with E C with E and D with E Using BH method in LIMMA analysis how do I carry out a time series analysis of this time course data? Any useful suggestions in the area of matrix design and useful codes would be greatly appreciated. Yemi PhD student

>the design matrix is such that I compared each total replicate in >the treatment i.e A, B, C, and D with E. Thus > >A is compared with E >B with E >C with E >and D with E > >Using BH method in LIMMA analysis how do I carry out a time series >analysis of this time course data? >Any useful suggestions in the area of matrix design and useful codes >would be greatly appreciated. Hi Yemi, You have a common reference design. Have you read through the limma vignette? Try: >limmaUsersGuide() See section 7.3 Common Reference Designs on how to create a design matrix where each treatment A-D is represented by a column. From there, you can go into section 8.8 Time Course Experiments to see how to create a contrast matrix to compare specific time points and/or use topTableF() to find genes that change over any time point. HTH, Jenny >Yemi >PhD student > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu