Difference between revisions of "Laurmagee: Individual Assessment"

Revision as of 00:21, 13 December 2013

Statement of Work

• Describe exactly what you did on the project.
• The first step in my role as GenMAPP user was to find an article that contained microarray data on the Rhizobacterium, Sinorhizobium Meliloti. I submitted a few articles for consideration, but ultimately my partner, Miles, found the article we have been using throughout this project. The mentioned article can be found on the following page: [HTML version] and is references below.
• Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti Journal of Bacteriology 188:7617-7625
• From this article, we were able to procure the raw microarray data off of the following website: [Osmotic upshift elicited by salt and sucrose].
• The article that we were studying carried out four different experiments, with different levels of NaCl and sucrose being the manipulated variable. I personally studied the experiment done with 700mm of sucrose. Raw Data File for 700S (1-3): File:Full Raw Data.xls
• The columns of interest in the above data file were collect and scaling and centering was done to produce the log values needed for statistical analysis. Further description can be found on the following page: Laurmagee: Week 13. And the following data file was produced Media:Compiled Ratios and Logs.xls.
• With this new file, statistical analysis could be done on the log values. Fist the Avg_LogFC values were calculated, averaging the log values of the three replicants present at each of the four individual time intervals (t15, t30, t60, t240). Therefore, I had to calculate four of these Avg_LogFC values, one for each time point. From these averages, I was able to calculate the T_stat and P_value for each time interval as well. This process if outlined in the "Statistical Analysis" section of the following journal: Laurmagee: Week 15. This spreadsheet was formatted specifically for GenMAPP standards and the following were produced: Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls and Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt. The text file is to be fed into GenMAPP.
• A Sanity Check was done and highlighted on the following page: Laurmagee: Week 15, and it shows the number of microarray dots that were changed significantly in the process of the experiment.
• After this check proved to provide accurate results, I moved on to load my datafile into GenMAPP. However, this is where I found a snag. My GenMAPP file would not load into GenMAPP and the whole program would stop responding immediately after I would input my text file.
• After trying different computer, walking through every aspect of my data file with my partners, and trouble shooting different alternatives, I finally emailed Dr. Dondi, who found the main problem with my dataset. The gene IDs that had been present on my sheet did not follow the same format of those in the Gene Database that was created by my partners. The paralleled IDs were present, but they had extraneous information attached to them, which was inhibiting GenMAPP from recognizing them. The amount of error that the file was collecting was so large that the program had to stop responding entirely, which is why I wasn't getting an error message.
• However, even upon testing the modified data sheet, I found that it was giving me another error message. This time it was telling me my column titles were insufficient. After some research, I found that my text file was not in tab delimited format, despite the fact that I had saved it as such on my MacBook Pro computer. After transferring my previous .xls workbook onto a Windows computer, and saving it as a tab delimited text file, I finally got GenMAPP to accept the following data file: Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt.
• The GenMAPP and MAPPFiner protocols can be viewed at the bottom of the following journal page: Laurmagee: Week 15.
• The exception file created with the GenMAPP program is included here: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.EX.txt] along with the following other three GenMAPP program exports: Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gex, [[Media:ColorSets.mapp]}, Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gmf, which are all detailed on the journal page noted above.
• In addition, the MAPPFinder documents are the following: Media:700S1-3-t15-Decreased-Criterion0-GO.txt, Media:700S1-3-t15-Increased-Criterion0-GO.txt
• Beyond my assigned tasks, I helped my group out in whatever areas were necessary. It was a challenge to keep up with the tasks of my partners, but I was always accessible to offer input or advice.

Assessment of Project

• Give an objective assessment of the success of your project workflow and teamwork.
  1. What worked and what didn't work?
  2. What would you do differently if you could do it all over again?
• Evaluate the Gene Database Project and Group Report in the following areas:
  1. Content: What is the quality of the work?
  2. Organization: Comment on the organization of the project and of your group's wiki pages.
  3. Completeness: Did your team achieve all of the project objectives? Why or why not?

Reflection on the Process

• What did you learn?
  1. With your head (biological or computer science principles)
  2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
  3. With your hands (technical skills)?
• What lesson will you take away from this project that you will still use a year from now?