How to carry out time series analysis in Bioconductor
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yemi yomi ▴ 50
@yemi-yomi-2895
Last seen 9.6 years ago
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
Microarray limma Microarray limma • 1.1k views
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 22 hours ago
United States
>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
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