BIOL367/F10:Class Journal Week 8

Andrew Herman Reflection Questions

• What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not?- Since I have done similar computations to this type of data in the past, I was fairly comfortable with the type of manipulations that we were preforming this week. Although this week I did learn some new tricks about Excel that will assist me in making the processing of the data faster an more efficient in the future.
• What advice would you give next year's class when performing this assignment?- Take your time, and be careful that you are performing the right manipulations on the right data. It can become very easy to get lost in all the numbers and forget what you should be doing. Especially when passing the data through various programs, it can also be easy to lose track of files if they are not given a detailed name that describes what is contained and when it was last modified.
• Do you think the original authors of the Merrell et al. (2002) paper adequately discussed their methods and results of their data analysis in their Nature paper? Why or why not? - In terms of their biological manipulations and methods, the paper in my view adequately describes the purpose and the explanation of their tests. It takes the reader through a step by step reasoning and explanation of each test. In terms of the actual data derived from these experiments and the manipulations performed upon them, the description was vague and poorly worded. They explained that they conducted a two class SAM analysis for each strain of VC, but they never described why they chose the cut off of a two fold expression change to be significant. In my view, this cutoff seemed somewhat of an arbitrary point chosen by the researchers and did not encompass all the information derived from the tests. Through this approximation they gave a list of genes that they claim were differentially expressed in the stool sample, such as VC0028. Due to the fact that they never truly explained step by step, their data manipulations and the way that they were interpreted, I believe that the Merrell paper did not adequately discuss their data analysis.

Andrew Herman 18:47, 23 October 2010 (EDT)

Richard Brous Reflection Questions

• What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not? - I used to use excel often but then have had a long stretch of not using it. Comfort level of conceptual use was high but only medium for practical use. Now that I've been through the exercise I am all warmed up and ready for statistical analysis!
• What advice would you give next year's class when performing this assignment? I would be sure to have access to the professors when setting up the layout of the worksheets to avoid confustion. The written instructions can take several readings to be sure of what to do and any mistake will affect the later worksheets causing you great pains...
• Do you think the original authors of the Merrell et al. (2002) paper adequately discussed their methods and results of their data analysis in their Nature paper? Why or why not? In regards to their specific process of normalization and statistical analysis it isn't clear exactly what they did. This would make duplication of their work by others difficult. Additionaly they used a software application but didn't share any default or specific setting which might affect how it would return results.

Richard Brous 20:44, 23 October 2010 (EDT)

Salomon Garcia

• What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not?----My initial comfort with using excel was quite good this was due to doing similar analysis in the previous semester. Once I began doing the assignment the juices started to flow and things began to coming back on how to do the analysis. I felt that my comfort level remained the same since this was a review of procedures that I previously learned.
• What advice would you give next year's class when performing this assignment?----I would tell next years class to ask questions and to email the professors if they are not understanding some of the material that is being asked for. For example I had some trouble when it came to find the p-values it wasn't until I read the instructions several times until I was able to figure out how to input the information into excel. So ask questions and send emails would be my advise.
• Do you think the original authors of the Merrell et al. (2002) paper adequately discussed their methods and results of their data analysis in their Nature paper? Why or why not?----I feel that the authors of the Merrell et al. paper needed to have discussed there methods and there data on there paper more extensively, as I read the paper there were portions that this information would have been beneficial and easier to understand what the authors were presenting. I felt that the paper that was published in Nature just represented a fraction of the overall process and findings that they made, more information was needed to better understand there results.

Salomon Garcia Valencia 03:20, 24 October 2010 (EDT) BIOL367/F10 Week 8 Assignment Link