*Download the file '''Merrell_Compiled_Raw_Data_Vibrio.xls''' from the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Microarray Analysis for ''Vibrio cholerae'' page].

*Download the file '''Merrell_Compiled_Raw_Data_Vibrio.xls''' from the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Microarray Analysis for ''Vibrio cholerae'' page].

**Save the file with the following format for the filename: Merrell_Compiled_Raw_Data_Vibrio_<Initials>_<Date>.xls

**Save the file with the following format for the filename: Merrell_Compiled_Raw_Data_Vibrio_<Initials>_<Date>.xls. In my case, the filename is "Merrell_Compiled_Raw_Data_Vibrio_KS_20131010.xls".

*This file contains the Log₂ of Red Dye/Green Dye Normalized Ratio (Median) organized in the following manner:

*This file contains the Log₂ of Red Dye/Green Dye Normalized Ratio (Median) organized in the following manner:

**'''Patient A'''

**'''Patient A'''

*Go back to the "scaled_centered" worksheet and Select All and Copy the scaled and centered data.

*Go back to the "scaled_centered" worksheet and Select All and Copy the scaled and centered data.

:*To do so, click on the first cell of the data (cell O4). Then hold the Shift and Ctrl keys, hit the Right Arrow key, and then hit the Down Arrow key (making sure that you are still holding down the Shift and Ctrl keys). Then, Copy the selection.

:*To do so, click on the first cell of the data (cell O4). Then hold the Shift and Ctrl keys, hit the Right Arrow key, and then hit the Down Arrow key (making sure that you are still holding down the Shift and Ctrl keys). Then, Copy the selection.

*Go to the "statistics" worksheet and right click on cell B2. Go to the "Paste Special" option. A window will open: click on the radio button for "Values" and click OK. This pastes the data as numerical values rather than equations.  

*Go to the "statistics" worksheet and right click on cell B2. Highlight the "Paste Special..." option and then click on "Paste Special...". A window will open: click on the radio button for "Values" and click OK. This pastes the data as numerical values rather than equations.

*To the right of the data you just pasted into the worksheet, type the following headers into the first cell of the next three columns: "Avg_LogFC_A", "Avg_LogFC_B", and "Avg_LogFC_C".

*To the right of the data you just pasted into the worksheet, type the following headers into the first cell of the next three columns: "Avg_LogFC_A", "Avg_LogFC_B", and "Avg_LogFC_C".

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

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

*Now, compute a T statistic to determine how much the average log fold change of all the patients deviates from 0, which corresponds to now change. Type the header "Tstat" into the first cell in the next empty column (column R). Type the following equation into cell R2:

*Now, compute a T statistic to determine how much the average log fold change of all the patients deviates from 0, which corresponds to now change. Type the header "Tstat" into the first cell in the next empty column (column R). Type the following equation into cell R2:

  =Q2/(STDEV(N2:P2)/SQRT(COUNT(N2:P2))

  =Q2/(STDEV(N2:P2)/SQRT(COUNT(N2:P2))

:and hit enter. (The command COUNT() counts the number of patients in the experiment.)

:and hit Enter. (The command COUNT() counts the number of patients in the experiment.)

:*Double click on the lower right hand corner of cell R2 to compute the T statistic for the remainder of the genes.

:*Double click on the lower right hand corner of cell R2 to compute the T statistic for the remainder of the genes.