Lab7 - CSci 3003: Introduction to Computing in Biology Lab...

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CSci 3003: Introduction to Computing in Biology Lab Assignment #7 20 points Assigned: 3/24/10 Due: Tuesday, 4/6/10 (before midnight) Goals of this lab: Practice using Matlab to load/analyze data. Learn about statistical analyses of gene expression data. Lab 7: Statistical analysis of gene expression data in Matlab This homework will focus on statistical analysis of gene expression data. Specifically, we will investigate genes that are associated with the development of metastases from primary breast tumors. The data from this lab are taken from the following study, which you can read about by clicking http://www.nature.com/nature/journal/v415/n6871/abs/415530a.html : “Gene expression profiling predicts clinical outcome of breast cancer.” Nature 415, 530-536 (31 January 2002). van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH.
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Part I: Understanding the breast cancer study This week’s lab will focus on understanding the dataset, loading the data into Matlab, and doing some simple manipulations of the data. Before we begin doing statistical analyses of the gene expression data, it is important that you take some time to understand the study. By following the link above (or simply using Google to find the study), open the paper associated with the data and read the paper’s abstract. Briefly answer the following questions about the study: (1) What was the purpose of the study and what experiments did the authors do to answer the question they were interested in? (2) What two sets of tumor samples did the authors profile for gene expression? (3) Describe one of the significant conclusions of the study. Part II: Loading and manipulating expression data in Matlab (1) We have provided three data files for this lab: The actual expression data (24481 genes X 78 samples) http://www- users.itlabs.umn.edu/classes/Spring-2010/csci3003/files/lab7/vantVeer_expression_data.txt
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This note was uploaded on 10/21/2011 for the course CSCI 3003 taught by Professor Staff during the Spring '08 term at Minnesota.

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Lab7 - CSci 3003: Introduction to Computing in Biology Lab...

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