=== Perform statistical analysis on the ratios ===

=== Perform statistical analysis on the ratios ===

We are going to perform this step on the scaled and centered data you produced in the previous step.

I performed this step on the scaled and centered data I produced in the previous step.

* Insert a new worksheet and name it "statistics".

* I inserted a new worksheet and named it "statistics".

* Go back to the "scaling_centering" worksheet and copy the first column ("ID").

* I went back to the "scaling_centering" worksheet and copied the first column ("ID").

* Paste the data into the first column of your new "statistics" worksheet.

* I pasted the data into the first column of my new "statistics" worksheet.

* Go back to the "scaling_centering" worksheet and copy the columns that are designated "_scaled_centered".

* I went back to the "scaling_centering" worksheet and copied the columns that were designated "_scaled_centered".

* Go to your new worksheet and click on the B1 cell.  Select "Paste Special" from the Edit menu.  A window will open: click on the radio button for "Values" and click OK.  This will paste the numerical result into your new worksheet instead of the equation which must make calculations on the fly.

* I went to my new worksheet and clicked on the B1 cell.  I selected "Paste Special" from the Edit menu.  A window opened: I clicked on the radio button for "Values" and clicked OK.  This pasted the numerical result into my new worksheet instead of the equation which must have made calculations on the fly.

* Delete Rows 2 and 3 where it says "Average" and "StDev" so that your data rows with gene IDs are immediately below the header row 1.

* I deleted Rows 2 and 3 where it said "Average" and "StDev" so that my data rows with gene IDs were immediately below the header row 1.

* Go to a new column on the right of your worksheet.  Type the header "Avg_LogFC_A", "Avg_LogFC_B", and "Avg_LogFC_C" into the top cell of the next three columns.

* I went to a new column on the right of my worksheet.  I typed the header "Avg_LogFC_A", "Avg_LogFC_B", and "Avg_LogFC_C" into the top cell of the next three columns.

* Compute the average log fold change for the replicates for each patient by typing the equation:

* I computed the average log fold change for the replicates for each patient by typing the equation:

  =AVERAGE(B2:E2)

  =AVERAGE(B2:E2)