Monica Hong Electronic Journal Edit

Microarray Data Analysis

• Edited on 05/18/15, 05/19/15

Viewing File Extensions

• The Windows 7 operating systems defaults to hiding file extensions. To turn them back on, do the following:
• Go to the Start menu and select "Control Panel".

1. In the window that appears, search for "Folder Options" in the search field in the upper right hand corner.
2. Click on "Folder Options" in the main window.
3. When the Folder Options window appears, click on the View tab.
4. Uncheck the box for "Hide extensions for known file types".
5. Click the OK button.

Set Your Browser to Prompt You for the Location to Save your Downloaded Files

• In Google Chrome, open the Settings window.
• Click on the link at the bottom of the page that says "Advanced Settings".
• Scroll down to "Downloads" and check the box that says "Ask where to save each file before downloading".
• You could also change the default Download location to your Desktop, so that will be the first choice when it prompts you where to save the file.
• Your settings are automatically saved.

Steps 1-3: Generating Log2 Ratios with GenePix Pro

• The protocol for gridding and generating the intensity (log2 ratio) data with GenePix Pro 6.1 is found on [[1]].
• This protocol will generate a *.gpr file for each chip which is then fed into the normalization protocol below.

Steps 4-5: Within- and Between-chip Normalization

• Installing R 3.1.0 and the limma package

• The following protocol was developed to normalize GCAT and Ontario DNA microarray chip data from the Dahlquist lab using the R Statistical Software and the limma package (part of the Bioconductor Project).
  • The normalization procedure has been verified to work with version 3.1.0 of R released in April 2014 ([[2]]) and and version 3.20.1 of the limma package (Limma.3.20.1.zip) on the Windows 7 platform.
    • Note that using other versions of R or the limma package might give different results.
    • Note also that using the 32-bit versus the 64-bit versions of R 3.1.0 will give different results for the normalization out in the 10-13 or 10-14 decimal place. The Dahlquist Lab is standardizing on using the 64-bit version of R.
  • To install R for the first time, download and run the installer from the link above, accepting the default installation.
  • To use the limma package, unzip the file and place the contents into a folder called "limma" in the library directory of the R program. If you accept the default location, that will be C:\Program Files\R\R-3.1.0\library (this will be different on the computers in S120 since you do not have administrator rights).

Running the Normalization Scripts

• Create a folder on your Desktop to store your files for the microarray analysis procedure.
• Download the zipped file wt-dCIN5-dGLN3-dHAP1-dHMO1-dSWI4-dZAP1-Spar_gpr-files.zip that contains the .gpr files and save it to this folder (or move it if it saved in a different folder).
  • Unzip this file using 7-zip. Right-click on the file and select the menu item, "7-zip > Extract Here".
• Download the GCAT_Targets.csv file GCAT_Targets.csv and Ontario_Targets_wt-dCIN5-dGLN3-dHAP4-dHMO1-dSWI4-dZAP1-Spar_20150514.csv files and save them to this folder (or move them if they saved to a different folder).
• Download the Ontario_Chip_Within-Array_Normalization_modified_20150514.R and save (or move) it to this folder.
• Download the Within-Array_Normalization_GCAT_and_Merged_Ontario-GCAT_Between-Chip_Normalization_modified_20150514.R script and save (or move) it to this folder.

P-value tables for dHAP4 strain

PvaluesMH051915_table.pptx