Jkuroda Week 8

Normalized the log ratios for the set of slides in the experiment

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

Inserted a new Worksheet into my Excel file, and named it "scaled_centered".
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.
Inserted two rows in between the top row of headers and the first data row.
In cell A2, typed "Average" and in cell A3, typed "StdDev".
I computed the Average log ratio for each chip (each column of data). In cell B2, I typed the following equation:

=AVERAGE(B4:B5224)

and pressed "Enter". Excel computed 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.

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)

and pressed "Enter".

Excel then did some of the work for me. I copied these two equations (cells B2 and B3) and pasted them into the empty cells in the rest of the columns. Excel automatically changed the equation to match the cell designations for those columns.
I have now computed the average and standard deviation of the log ratios for each chip. Now I actually did the scaling and centering based on these values.
I copied the column headings for all of my data columns and pasted them to the right of the last data column so that I had a second set of headers above the blank columns of cells. I edited the names of the columns so that they read as: A1_scaled_centered, A2_scaled_centered, etc.
In cell N4, I typed the following equation:

=(B4-B$2)/B$3

In this case, I wanted the data in cell B4 to have the average subtracted from it (cell B2) and be divided by the standard deviation (cell B3). I used the dollar sign symbols in front of the "2" and "3" to tell Excel to always reference that row in the equation, even though I pasted it for the entire column of 5221 genes.

I copied and pasted this equation into the entire column.
I then copied and pasted the scaling and centering equation for each of the columns of data with the "_scaled_centered" column header.

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