User:Kam D. Dahlquist/Notebook/Personal/2011/07/20

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I am following the updated Microarray Data Processing in R protocol created by Nick and Katrina.

R version

  • Use R version 2.7.2.
  • Instructions for installing R and packages are found here.

Normalization

First, target files must be created to input all of the GPR files into R. In order to do so, open up Microsoft Excel. The first column should be labeled "FileName", consisting of all the GPR file names. This should be followed by a column labeled "Header" that has the column names for the GPR files, then "Strain", "TimePoint", "Flask", and "DyeSwap" for each GPR. Make sure they match up to their respective GPR files in the excel sheet and save this as a CSV file. Repeat this step for the GCAT chips, placing the top nine chips in the row 2-10 and the bottom nine in rows 11-19. You will also need to load a CSV file containing the gene IDs into R for both the Ontario and GCAT chips. This can be accomplished by running a single GPR file through R until you duplicate the spots. This is where R alphabetizes the IDs and their corresponding spots with them, this can then be saved to a table and copied to a new CSV file. This file can be loaded into R and used to add the gene IDs to the data. Use these lines of code:

To Do