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Right-click on the file and select the menu item, "7-zip > Extract Here". gpr files and save it to this folder (or move it if it saved in a different folder). Download the zipped file wt-dCIN5-dGLN3-dHAP1-dHMO1-dSWI4-dZAP1-Spar_gpr-files.zip that contains the.Create a folder on your Desktop to store your files for the microarray analysis procedure.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). 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.

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To install R for the first time, download and run the installer from the link above, accepting the default installation.

The Dahlquist Lab is standardizing on using the 64-bit version of R.

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.

Note that using other versions of R or the limma package might give different results.

The normalization procedure has been verified to work with version 3.1.0 of R released in April 2014 (]) and and version 3.20.1 of the limma package ( Limma.3.20.1.zip) on the Windows 7 platform.

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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).

Installing R 3.1.0 and the limma package.

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

This protocol will generate a *.gpr file for each chip which is then fed into the normalization protocol below.

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The protocol for gridding and generating the intensity (log2 ratio) data with GenePix Pro 6.1 is found on ].Steps 1-3: Generating Log2 Ratios with GenePix Pro 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.Scroll down to "Downloads" and check the box that says "Ask where to save each file before downloading".Click on the link at the bottom of the page that says "Advanced Settings".In Google Chrome, open the Settings window.Set Your Browser to Prompt You for the Location to Save your Downloaded Files Uncheck the box for "Hide extensions for known file types".When the Folder Options window appears, click on the View tab.Click on "Folder Options" in the main window.In the window that appears, search for "Folder Options" in the search field in the upper right hand corner.Go to the Start menu and select "Control Panel".The Windows 7 operating systems defaults to hiding file extensions.

11.3 Sanity Check: Number of genes significantly changed.11.2 Calculate the Benjamini & Hochberg p value Correction.11.1 Calculate the Bonferroni and p value Correction.9.1 Visualizing the Normalized Data Create MA Plots and Box Plots for the Ontario Chips.8 Within Array Normalization for the GCAT Chips and Between Array Normalization for All Chips.7 Within Array Normalization for the Ontario Chips.5 Steps 4-5: Within- and Between-chip Normalization.4 Steps 1-3: Generating Log2 Ratios with GenePix Pro.3 Set Your Browser to Prompt You for the Location to Save your Downloaded Files.