Latest revision as of 04:50, 24 November 2015

Lena Olufson

• Link to team page: https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/The_Class_Whoopers

Week 12

• This week there were no specific tasks that were required to be completed; instead the assignment is to keep on working on the team projects and what each specific role should be doing.
• After analyzing the microarray paper last week, Mahrad and I were then able to start analyzing the data.

GenMAPP User

Locating the Sample Data

• The first step in the data retrieval was to locate the sample files that needed to be downloaded from the microarray paper site, found at: [1].
  • Dr. Dahlquist assisted me (and Mahrad) in choosing which files to download as well as how to prepare them for Excel.
  • All of the six sample files were downloaded from this site and saved to the computer.
• Then each of the files were unzipped once, and then unzipped again in order to access them in a suitable manner for the assignment, which in this case was being able to open the files in Exel.
  • Once all six of the files were unzipped, I opened each of them in Excel in order to get the data in the column spreadsheet form.

Working with the data in Excel

• I created a new workbook that would contain the final compressed data that is to be eventually exported as one file.
  • After opening each of the sample files in Excel, I copied the list of Gene IDs from one of the samples (they are the same in all of the samples) and pasted it into the new workbook I started.
  • Now that the Gene ID column was formed, I was then able to start pasting the desired data columns in from each of the different samples.
  • From each of the six samples, I copied and pasted the "Log Ratio" column into my new workbook and titled each of the columns so that they represented the appropriate samples in an orderly fashion.
• Now that all of the data is compiled into a worksheet, my next task is to perform the correct data manipulations and corrections in order to make the data file ready to be exported for testing and analysis.
  • Mahrad and I completed these construction steps side-by-side and we plan on continuing the Excel work together in order to check our work.
• The current Excel data worksheet we have constructed: File:Bpertussis CompiledRawData MS2015.xlsx

Gene Database Testing (Coder)

• I assisted Brandon this week with a section of the Gene Database Testing Report as Nicole is still absent from class.
  • Gene Database Testing Report- cw20151119 (Brandon authored sections 1-4.6. I authored sections 4.7 & 4.8)

Loyola Marymount University: website