790391 Efficient microarray data analysis using R and FSPMA

Type
Lecture and exercise
Semester hours
1
Lecturer (assistant)
Organisation
Offered in
Wintersemester 2022/23
Languages of instruction
Englisch
Content

The theory part of the lecture includes the following topics:
1) microarray normalization,
2) mixed effects ANOVA models,
3) ANOVA tables,
4) experimental designs,
5) specifying contrasts for comparisons,
6) adjustments for multiple comparisons,
7) setting up FSPMA for analysis of single and two color arrays,
8) visualizations of microarray data with FSPMA
9) combining FSPMA with external libraries.

The practical part of the lecture gives students the opportunity to analyse two publicly available microarray data sets for differentially expressed genes. The exercises cover all aspects of microarray analysis listed above and will in addition highlight the effects of altering analysis steps like the chosen normalization method. The practical work constitutes an essential part of the evaluation. The overall assessment is based on a laboratory protocol which we will discuss in a group session to determine the final mark.
Previous knowledge expected

The successful completion of the lecture depends on a basic knowledge of statistics and requires proficiency with using computers.
Objective (expected results of study and acquired competences)

Successful completion of the lecture enables students to analyse microarray experiments efficiently with the statistics package R and the FSPMA library. Participants will understand the theoretical concepts of statistical testing and ANOVA models in particular. Students will furthermore be able to analyse simple microarray experiment designs with R and provide useful graphical visualizations. Successful participants will in addition be able to independently familiarize themselves with sophisticated data analysis libraries such as for example provided in the Bioconductor archive.
You can find more details like the schedule or information about exams on the course-page in BOKUonline.