Materials for CLASS05

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Affymetrix Power Tools (APT) User Guide Link

Affymetrix Homepage Link

Register to Login and download APT and CDF files.


  • Download KRAS-dependency data example here

    1. Unzip and untar the KRAS-dependency data from DATA_FOR_CLASS06.tar.gz.
    2. 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.
    3. Make a folder of RMA_OUTPUT in the DATA_FOR_CLASS06 directory.
    4. Perform apt-probeset-summarize on the CEL files and output the results in RMA_OUTPUT.
      See slides for details

    Assignment #6

    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:

    1. Download GSE18088 Raw data from NCBI GEO.
    2. Extract the data using APT (Get CDF file from Affymetrix website).
    3. 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%.
    4. Plot the differentially expressed genes as heat map using matrix2png.

    5. Send me the list of differentially expressed genes and heat map.