=== Normalize the log ratios for the set of slides in the experiment ===

=== Normalize the log ratios for the set of slides in the experiment ===

To scale and center the data (between chip normalization) perform the following operations:

I scaled and centered the data (between chip normalization) by performing the following operations:

* Insert a new Worksheet into your Excel file, and name it "scaled_centered".

* Inserted a new Worksheet into my Excel file, and named it "scaled_centered".

* Go back to the "compiled_raw_data" worksheet, Select All and Copy.  Go to your new "scaled_centered" worksheet, click on the upper, left-hand cell (cell A1) and Paste.

* Went back to the "compiled_raw_data" worksheet, Selected All and Copy.  Went to my new "scaled_centered" worksheet, clicked on the upper, left-hand cell (cell A1) and Pasted.

* Insert two rows in between the top row of headers and the first data row.

* Inserted two rows in between the top row of headers and the first data row.

* In cell A2, type "Average" and in cell A3, type "StdDev".

* In cell A2, I typed "Average" and in cell A3, typed "StdDev".

* You will now compute the Average log ratio for each chip (each column of data).  In cell B2, type the following equation:

* I went to compute the Average log ratio for each chip (each column of data).  In cell B2, I typed the following equation:

  =AVERAGE(B4:B5224)

  =AVERAGE(B4:B5224)

: and press "Enter".  Excel is computing the average value of the cells specified in the range given inside the parentheses.  Instead of typing the cell designations, you can click on the beginning cell, scroll down to the bottom of the worksheet, and shift-click on the ending cell.

: and pressed "Enter".  Excel computer the average value of the cells specified in the range given inside the parentheses.  Instead of typing the cell designations, I clicked on the beginning cell, scrolled down to the bottom of the worksheet, and shift-clicked on the ending cell.

* You will now compute the Standard Deviation of the log ratios on each chip (each column of data).  In cell B3, type the following equation:

* I then computed the Standard Deviation of the log ratios on each chip (each column of data).  In cell B3, I typed the following equation:

  =STDEV(B4:B5224)

  =STDEV(B4:B5224)