BIOL367/F10:Class Journal Week 8

Andrew Herman Reflection Questions
Andrew Herman 18:47, 23 October 2010 (EDT)
 * 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.

Richard Brous Reflection Questions
Richard Brous 20:44, 23 October 2010 (EDT)
 * 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.

Salomon Garcia
Salomon Garcia Valencia 03:20, 24 October 2010 (EDT)
 * 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.

Andrew Forney
Andrew Forney 06:14, 24 October 2010 (EDT)
 * What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not? Previous to the assignment, my experience with Excel was fairly rudimentary; I knew how to navigate it and use functions, define ranges, etc., but this exercise exposed some of its more powerful tools, like filters, that were then new to me. I do feel an increased level of comfort now knowing more about its functionality.
 * What advice would you give next year's class when performing this assignment? In my honest opinion (and I don't intend to sound cocky), this was the easiest assignment that we've had to date. As such, my advice to next year's class would be to look forward to this one! Short of that, I suppose my next best piece of advice would be to learn keyboard shortcuts like the back of your hand or it could potentially take some time.
 * 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? Yes, I think their discussion was adequate because they assumed a certain familiarity of their audience with the topic and traditional methods of discerning the results; in other words, this was not an article aimed at students just learning about microarray analysis, it was to associates in the field who have had much more experience--as such, this allows the authors to breeze over some (not so obvious to us) details. If I were to critique it from my own viewpoint, I would say that there wasn't enough information as to step-by-step process, nor the statistical analysis and means of performing it--but I'd rather be completely objective about it and cut them some slack!

Jennifer Okonta
Jennifer Okonta 18:45, 24 October 2010 (EDT)
 * 1) What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not? I was not that experienced with working with excel but i knew how to use it to a certain extent. I was able to do simple things like the average and filling in cells but that was the most i could do by myself. Putting in the other equations took practice and after doing it multiple time on the homework assignment, I am more comfortable working with excel.
 * 2) What advice would you give next year's class when performing this assignment?Just relax and follow the directions. They really are self explanatory and it will not take you long to finish the homework assignment.
 * 3) 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? Yes because experienced biologists would know and understand everything that the was being written about. They gave clear enough explanations and describe their methods in a way a clear that was clear enough for them to understand.

Claudia Campos
Claudia Campos 19:47, 24 October 2010 (EDT)
 * 1) What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not? I was pretty comfortable with excel, but not in the ways used for this assignment. I had never used the filter or the some of the functions used in this week. I was comfortable in making graphs, getting the best fit line, finding the standard deviation, finding R squared values, and some other functions. My comfort level definitely increased because now I am aware of other powerful tools excel has to offer.
 * 2) What advice would you give next year's class when performing this assignment? I'd say just to take it slow, so as to not make mistakes and understand what's being done. It's not too difficult, but it does take patience.
 * 3) 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? I'd say they did since their audience is other scientists or people well-versed in what is being discussed, so they didn't find it necessary to go too much into detail. For students, such as ourselves in our class, it would've been better for the paper to have gone in a little more detail, rather than just saying details are found elsewhere.

Zeb Russo
Zeb Russo 22:35, 24 October 2010 (EDT)
 * What was your initial comfort level with Excel before performing this exercise? Did your comfort level change?  Why or why not? - I was very comfortable with Excel before this assignment and it only rose slightly since I learned a couple new tricks regarding filters and performing calculations within boxes.
 * What advice would you give next year's class when performing this assignment? - Just stick to the directions and you'll be fine. Make sure to double check your work, and save often.
 * 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? - When Merrell et al talks about the biological methods for the finding of their data they are quite specific, however when it came to the manipulation of the raw data, they became somewhat vague and difficult to follow. If I was trying to do this from scratch and following their methods instead of the one set out by Dondi and Dahlquist, I would have been much more confused and would have taken me much longer to complete.

Evan Montz

 * What was your initial comfort level with Excel before performing this exercise? Did your comfort level change?  Why or why not?-- My engineering classes have required me to use excel relatively often in the past so I came into this assignment pretty comfortable with Excel.  I learned a couple of new things such as special pastes and filtering data which can be very useful.  I would say my comfort level hasn't really changed but I did learn a couple of new helpful tools.
 * What advice would you give next year's class when performing this assignment?-- Follow the directions and allow enough time to finish. Everything is pretty straightforward but it is very time consuming.
 * 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 think the key to the quality of their explanation is dependent on the intended audience.  If the audience is intended to be very knowledgeable on the subject, I think it is fine for them to be vague with the description of their methods as they sort of were.  I think that this article wasn't intended to inform undergraduate students so I think the methods were adequately discussed.

Evan Montz 23:14, 24 October 2010 (EDT)

Margie Doyle
Margie Doyle 02:50, 25 October 2010 (EDT)
 * What was your initial comfort level with Excel before performing this exercise? Did your comfort level change?  Why or why not? - I have had no previous experience with Excel, and this served to frustrate me more than anything.  I understand some things about Excel now, but overall I would like to stay as far away from Excel as possible.
 * What advice would you give next year's class when performing this assignment? - Don't total your car when you need to finish it.
 * 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? - Most of this went right over my head to begin with, but I see the general intended direction, thanks to Dondi and Dahlquist's directions.

BIOL367/F10 Week 8 Assignment Link