Materials for CLASS05
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Workshop 6 - PROCESSING, QUERYING AND VISUALIZING GENE EXPRESSION DATA
Affymetrix Power Tools (APT) User Guide
Affymetrix Homepage Link
Register to Login and download APT and CDF files.
Download KRAS-dependency data example here
- Unzip and untar the KRAS-dependency data from DATA_FOR_CLASS06.tar.gz.
- Inside the DATA_FOR_CLASS06 folder, it contains 12 CEL files. These samples were profiled by Affymetrix HT-HGU133A microarray, and the corresponding CDF file is included.
- Make a folder of RMA_OUTPUT in the DATA_FOR_CLASS06 directory.
- Perform apt-probeset-summarize on the CEL files and output the results in RMA_OUTPUT.
See slides for details
So far, you have learned all the basic skills to perform microarray gene expression data analysis. A collaborator is interested in analyzing the data published in this paper. As a bioinformatician, you are being assigned to assist this collaborator in downloading the data, extracting, analyzing and visualizing the differentially expressed genes between "Disease-Free" (DF) and "Relapse" (R) colorectal cancer patients.
Your tasks are:
- Download GSE18088 Raw data from NCBI GEO.
- Extract the data using APT (Get CDF file from Affymetrix website).
- Perform Significance Analysis of Microarray on the data to find out the genes that were differentially expressed between "Disease Free" (DF) group and "Relapse" (R) group at FDR 10%.
- Plot the differentially expressed genes as heat map using matrix2png.
- Send me the list of differentially expressed genes and heat map.