Difference between revisions of "Stephen Louie Week 8"
From LMU BioDB 2013
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*Clicked on the B1 cell. Selected "Paste Special" from the Edit menu. Clicked on the radio button for "Values" and clicked OK. | *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 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. | ||
===Part 2=== | ===Part 2=== | ||
Revision as of 06:25, 18 October 2013
Contents |
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.
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
