Revision as of 07:43, 18 October 2013

Overview of Microarray Data Analysis

Lab Journal

Part 1

• Accessed BIOL398-01:Bioinformatics Laboratory
• Downloaded the Merrell_Compiled_Raw_Data_Vibrio.xls file to Desktop.
• File renamed Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.xls to reflect ownership and date
• Inserted a new Worksheet into Excel file, and named it "scaled_centered"
• Copied data from "compiled_raw_data" worksheet into "scaled_centered" worksheet
• Inserted two rows in between the top row of headers and the first data row.
  • Typed "Average" in cell A2 and "StdDev" in cell A3
• Typed "=AVERAGE(B4:B5224)" in cell B2.
• Typed "=STDEV(B4:B5224)" in cell B3.
• Copied both equations in cells B2 and B3 and pasted them into the empty cells in the rest of the columns.
• Copied the column headings for all data columns and then pasted them to the right of the last data column.
• Edited the names of the columns to A1_scaled_centered, A2_scaled_centered, etc.
• Typed "=(B4-B$2)/B$3" in cell N4.
• Copied and pasted equation into the entire column.
  • Copied and pasted the scaling and centering equation for each of the columns of data with the "_scaled_centered" column header.
• Created new worksheet "statistics".
• Copied the first column ("ID") of "scaling_centering" worksheet and pasted the data into the first column of "statistics" worksheet.
• Copied the columns that are designated "_scaled_centered" of "scaling_centering" worksheet
• Clicked on the B1 cell. Selected "Paste Special" from the Edit menu. Clicked on the radio button for "Values" and clicked OK.
• Typed the header "Avg_LogFC_A", "Avg_LogFC_B", and "Avg_LogFC_C" into the top cell of the next three columns.
• Typed "=AVERAGE(B2:E2)" into cell N2. Copied equation and pasted it into the rest of the column.
• Typed equation for Patients B & C and pasted it into their columns
• Typed the header "Avg_LogFC_all" into the first cell in the next empty column. Created equation to compute the average of the three previous averages and pasted it into entire column.
• Inserted a new column next to the "Avg_LogFC_all" column. Labeled the column "Tstat". Typed "=AVERAGE(N2:P2)/(STDEV(N2:P2)/SQRT(number of replicates))" Copied the equation and pasted it into all rows in that column.
• Labeled the top cell in the next column "Pvalue". In the cell below the label typed "=TDIST(ABS(R2),degrees of freedom,2)" Copied the equation and pasted it into all rows in that column.
• Created new worksheet "forGenMAPP".
• Selected All and Copy on the "statistics" worksheet
• Clicked on cell A1 of "forGenMAPP" and selected Paste Special, clicked on the Values radio button, and clicked OK.
• Selected Columns B through Q (all the fold changes). Selected the menu item Format > Cells. Under the number tab, selected 2 decimal places. Clicked OK.
• Selected Columns R and S. Selected the menu item Format > Cells. Under the number tab, selected 4 decimal places. Clicked OK.
• Selected Columns N through S and Cut. Selected Column B by left-clicking on the "B" at the top of the column. Then right-clicked on the Column B header and selected "Insert Cut Cells"
• Deleted Rows 2 and 3 where it says "Average" and "StDev".
• Inserted a column to the right of the "ID" column. Typed the header "SystemCode" into the top cell of this column. Filled the entire column (each cell) with the letter "N".
• Selected the menu item File > Save As, and chose "Text (Tab-delimited) (*.txt)" from the file type drop-down menu.

Part 2

Files

Part 1

Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.txt

Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.xls

Part 2

Increased_SL-Criterion0-GO.txt

Increased_SL-Criterion0-GO.xls

Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.EX.txt

Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.gex

Merrell_Compiled_Raw_Data_Vibrio_SL_10102013.gmf