Kzebrows Week 14

Electronic Lab Notebook

First, I downloaded the most recent version of the file from the OTS Files page. I renamed all columns by replacing LR with LogFC. I re-named Sheet 1 "CompiledRawData" and copied all of the data from it and pasted it into Sheet 2, which I re-named "MasterSheet". Next I:

• I deleted all ID columns except for column A, which I re-named "ID"
• I inserted a column to the left of column B and re-named it "MasterIndex"
• I typed "1" and cell B2 and 2 and Cell B3 and selected both cells. I double-clicked on the + sign to fill the entire column with numbers 1-4208.
• Selected the data and sorted A-->Z on the "ID" column
• Deleted rows that have "Empty" or "Blank####" ID. This left me with 3,926 files (3,927 minus 1 header row).
• Sorted by MasterIndex column to put IDs back in original order, smallest to largest.
• Replaced "Error" with nothing and got 585 replacements.
• Copy and pasted data into Sheet 3, which I re-named "ScalingCentering".

The next portion of the assignment was done by following the instructions in Sample Microarray Analysis Vibrio cholerae.

=Normalizing the log ratios for the set of slides in the experiment

• I inserted a new worksheet and named it Scaled_Centered
• I copied all data from the MasterSheet and pasted it into cell A1 of the Scaled_Centered sheet
• I inserted two rows in between the top row of headers and first data row. I named cell A2 "Average" and named cell A3 "StdDev".
• In cell C2 I typed =AVERAGE(C4:C3929) and in cell C3 I typed =STDEV(C4:C3929). I pressed enter and copied this equation across the rest of the columns through column AL.
• I then copied the column headings for all data columns and pasted them to the right of the last column. Using the copy/paste tool I renamed each column with "_Scaled_Centered" at the end.
• In cell AM4 I typed =(C4-C$2)/C$3 indicating that I wanted data in cell C4 to have the average subtracted from it and then to divide it by the standard deviation. I used the "$" sign to indicate that I did not want the average and standard deviation values to change even when the equation was pasted for the entire column of genes.
• I then copy and pasted that equation across the entire column by clikcing on the original cell and double-clicking on the black plus sign. I copy and pasted this equation for each column of the data.

Perform statistical analysis on the ratios

• I inserted a new worksheet and named it "Statistics"
• I copied and pasted the ID column from the ScalingCentering worksheet into the first column of the new worksheet
• I copied all Scaled_Centered columns from the ScalingCentering worksheet and pasted the values into column B1 of the new sheet
• Deleted "Average" and "StDev" columns