Difference between revisions of "Blitvak Week 8"

Revision as of 03:56, 24 October 2015

Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)

• Merrell_Compiled_Raw_Data_Vibrio.xls was downloaded, saved to the desktop, and renamed with some additional information (initials and the date)

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

The following operations were performed in order to scale and center the microarray data:

• The renamed Excel file was opened and a new Worksheet was inserted with the name scaled_centered
• Everything on the compiled_raw_data worksheet was selected and copied over to scaled_centered (formatting was the same, starting from the left-hand cell, A1)
• Two new rows were inserted between the top row of headers and the first data row in scaled_centered
• In cell A2, Average was typed in; in A3, StdDev was typed in
• The Average log ratio for each chip was computed by typing =AVERAGE(B4:B5224) into cell B2 and pressing enter
• The Standard Deviation of the log ratios on each chip was computed by typing =STDEV(B4:B5224) into cell B3 and pressing enter
• The equations in B2 and B3 were copied and pasted into the empty cells in the rest of the columns (A2 to C4)
• The column headings for all of the data columns were copied and pasted to the right of the last data column; this new set of headers was edited so that they read: A1_scaled_centered, A2_scaled_centered, etc.
• The equation =(B4-B$2)/B$3 was typed into cell N4; the dollar sign symbols were used in front of the "2" and "3" in order to ensure that Excel will not change the reference to that row when that same equation is pasted down the entire column of 5221 genes (this is important because the average and standard deviation is the same for the entire row, and therefore, the reference must stay the same). This equation is the scaling and centering equation.
• The scaling and centering equation was copied and pasted down the entire A1_scaled_centered by clicking the original cell with the equation and double-clicking the bottom right corner of the cell (cursor should change to a black plus sign prior to double-clicking)
• The scaling and centering equation was put in each of the data columns with the _scaled_centered header (was copied and pasted down the entire columns)
• The equation for each column was checked to ensure that it was correct (ex. for A2_scaled_centered, the equation should be =(C4-C$2)/C$3)

Performing statistical analysis on the ratios

the equation was also copied and pasted down the entire

• Modified Excel File/Data

• For GenMAPP

Working with: 2009 Vibrio Cholera database

• 772 errors were detected in the raw data by genMAPP using the 2009 database
• 121 errors were detected in the raw data by genMAPP using the 2010 database by my partner, Anindita V.

Results of 10/20 Work Session

.gex file for GenMAPP

Results of 10/22 Work Session

• Top 10 Ranked GO Terms

1. macromolecule metabolic process
2. localization
3. transporter activity
4. cellular macromolecule metabolic process
5. transport
6. establishment of localization
7. cell projection organization
8. cellular biopolymer metabolic process
9. macromolecule biosynthetic process
10. biopolymer metabolic process

• Analysis of the .EX.txt file produced by GenMAPP, via Excel, revealed that the 772 errors were: Gene not found in OrderedLocusNames or any related system; this suggests that the 2009 database did not

increased expression

Brandon Litvak
BIOL 367, Fall 2015