# BIOL398-01/S10:Class Journal Week 12

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(→Amanda Wavrin: added signature) |
Current revision (10:48, 20 April 2010) (view source) (→Janelle N. Ruiz) |
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==[[User:Angela A. Garibaldi | Angela Garibaldi]]== | ==[[User:Angela A. Garibaldi | Angela Garibaldi]]== | ||

==[[User: Alex J. George | Alex George]]== | ==[[User: Alex J. George | Alex George]]== | ||

+ | # This assignment's purpose was to further analyze the data that is associated with our paper by using the raw data and making our own calculations | ||

+ | # I definitely learned some useful shortcuts on Excel through this assignment. Also, it gave us the chance to see the kind of work that goes on behind the scenes of a scientific paper. I felt like our study wasn't even that comprehensive, but the amount of data associated with it was staggering. | ||

+ | # As for questions for this assignment, I am slowly understanding the calculations we are doing and the purpose behind them. However, I am still unsure of a proper experimental question to design our data analysis around. | ||

+ | [[User:Alex J. George|Alex J. George]] 02:47, 19 April 2010 (EDT) | ||

==[[User: J'aime C. Moehlman | J'aime Moehlman]]== | ==[[User: J'aime C. Moehlman | J'aime Moehlman]]== | ||

#The purpose of this assignment was to change the raw data we were given into the genMAPP formatted version and the sclaed versions that we will be using this week. We analyzed the formatted data by using excel. | #The purpose of this assignment was to change the raw data we were given into the genMAPP formatted version and the sclaed versions that we will be using this week. We analyzed the formatted data by using excel. | ||

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==[[User:Janelle N. Ruiz|Janelle N. Ruiz]]== | ==[[User:Janelle N. Ruiz|Janelle N. Ruiz]]== | ||

+ | #The purpose of this assignment was to prepare our excel data file of our gene data to be run for analysis on GenMAPP. | ||

+ | #This week we were able to reformat variables in our data file and we learned the best way to format them to run in GenMAPP. We also learned that sometimes data is not always self-explanotory (we could not figure out how the authors calculated key variables in our excel file. | ||

+ | #I had questions but KP answered them. | ||

+ | |||

+ | [[Janelle N. Ruiz Assignment 12]] | ||

+ | |||

==[[User:Bobak Seddighzadeh|Bobak Seddighzadeh]]== | ==[[User:Bobak Seddighzadeh|Bobak Seddighzadeh]]== | ||

+ | #What is the purpose of this assignment? The purpose of this assignment was to familiarize us with our dataset, and more importantly to conduct some t-tests and other calculations that will aid us in the design of our experiment. | ||

+ | #What did you learn? Firstly, I learned how to use excel much better. I learned how to find averages and t-tests and the mechanical aspects of using excel. | ||

+ | #Do you have any questions still? Some of the sanity check steps were a little hard to follow. I was not sure what an avergae log FC test was. | ||

+ | |||

+ | {{BobakS}} | ||

+ | |||

==[[User: Amanda N. Wavrin| Amanda Wavrin]]== | ==[[User: Amanda N. Wavrin| Amanda Wavrin]]== | ||

*[[Amanda N. Wavrin Week 12]] | *[[Amanda N. Wavrin Week 12]] | ||

*[[BIOL398-01/S10:Week 11|Week 12 Assignment Page]] | *[[BIOL398-01/S10:Week 11|Week 12 Assignment Page]] | ||

- | + | # The purpose of this assignment was to begin our work with our Merrel et al. ''Vibrio cholerae'' project. Completing this assignment allowed us to start working with our own DNA microarray data, the data that is specific to our paper on ''V. cholerae''. Our dataset is now in GenMAPP version so we will be able to use them in lab this week. | |

- | + | # While completing this assignment I got a much better understanding of how to analyze DNA microarray data while using excel. Not having a lot of background using excel, it was difficult to complete this assignment at first. After a little practice it became much easier. | |

- | + | # While following the instructions for this weeks assignment, I ran into some problems using excel. My computed p values did not match up with the expected results, leading me to beleive that I made a mistake along the way. I also had a difficult time creating and filling the "tstat" columns. | |

[[User:Amanda N. Wavrin|Amanda N. Wavrin]] 02:43, 19 April 2010 (EDT) | [[User:Amanda N. Wavrin|Amanda N. Wavrin]] 02:43, 19 April 2010 (EDT) | ||

==[[User: Ryan N. Willhite | Ryan Willhite]]== | ==[[User: Ryan N. Willhite | Ryan Willhite]]== | ||

+ | |||

+ | |||

+ | # What was the purpose of this assignment? The purpose of this assignment was to practice the analysis of DNA Microarray data in Xcel. It also gave us a chance to be proactive in inserting and organizing even more data that can be calculated using equations in excel to get average, standard deviation, etc. | ||

+ | # What did I learn from this assignment (head, hands, heart)? I learned how to input these equations to help organize as well as input more data to be analyzed. I also learned that simple changes in the equation can give false values which was a mistake pretty easy to make ; thank goodness for a partner. | ||

+ | # What did I not understand (yet) about this assignment? I still do not understand all of the reading of data and I do not understand why some values say "DIVO" and not able to derive some value, which caused some problems in averages, etc. | ||

+ | |||

+ | [[User:Ryan N. Willhite|Ryan N. Willhite]] 11:43, 19 April 2010 (EDT) | ||

+ | |||

+ | *[[BIOL398-01/S10:Week 12|Week 12 Assignment Page]] | ||

+ | |||

+ | *[[Ryan N. Willhite Week 12|Week 12 Journal]] | ||

+ | |||

==[[User:Kristoffer T. Chin | Kristoffer Chin]]== | ==[[User:Kristoffer T. Chin | Kristoffer Chin]]== | ||

#The purpose of this assignment was to help us understand the data that we are working with with the DNA Microarray. It helps organize the data and understand the meaning of the numbers that are given to us in the XLS files. WE are also able to understand what the researched are actually looking at and which are significants | #The purpose of this assignment was to help us understand the data that we are working with with the DNA Microarray. It helps organize the data and understand the meaning of the numbers that are given to us in the XLS files. WE are also able to understand what the researched are actually looking at and which are significants |

## Current revision

## Contents |

## Salomon Garcia

- The purpose of the assignment was to familiarize ourselves with the data gathered by van de Mortel et al. With there data we are to analyze the data in a way that has been showed to us by Dr. Dahlquist using Microsoft Excel.
- From this assignment I learned how to reuse some of the applications of excel and learned how to manipulate columns of data with a touch of button and inserting several formulas in order to come up with the data required for us to move forward.
- The only thing that I'm still a bit confused was if we are to do the log based function for all of the data acquired. Thus far that's what I've done to it.

(Salomon Garcia Valencia 23:35, 18 April 2010 (EDT))

## Angela Garibaldi

## Alex George

- This assignment's purpose was to further analyze the data that is associated with our paper by using the raw data and making our own calculations
- I definitely learned some useful shortcuts on Excel through this assignment. Also, it gave us the chance to see the kind of work that goes on behind the scenes of a scientific paper. I felt like our study wasn't even that comprehensive, but the amount of data associated with it was staggering.
- As for questions for this assignment, I am slowly understanding the calculations we are doing and the purpose behind them. However, I am still unsure of a proper experimental question to design our data analysis around.

Alex J. George 02:47, 19 April 2010 (EDT)

## J'aime Moehlman

- The purpose of this assignment was to change the raw data we were given into the genMAPP formatted version and the sclaed versions that we will be using this week. We analyzed the formatted data by using excel.
- This weeks assignment really gave me a chance to learn how to use excel. Parts of it were a little bit frustrating because I'm not very good at using excel other than for very basic functions, but I think that I did get a hang of it once I started.
- My concern for this weeks assignment has to do with the fact that I don't think I found the proper data, because while using the template on what to do, it said we should have about 261 genes and I only found 5. Also, I'm not sure what the Tstat columns were used for.

J'aime C. Moehlman 00:53, 19 April 2010 (EDT) Week 12 Assignment

## KP Ramirez

- The purpose of this assignment was to prepare our raw data into the formatted and scaled versions that would be used for next weeks GenMAPP program. This was different for me because I have never used Afymetrix data, so it was different to get used to what was already given and what was missing.
- This week allowed me to work with Excel again and format columns that were not specified to our data and create new ones. We redid some columns with a log base 2 as well as added the system code column and began formatting.
- I did have a couple of questions this week. I wasn't sure what columns would be used to do the Tstat as well as Pvalues.

KP Ramirez 7:14 am April 18 Individual week 12

## Michael Piña

1. The purpose of this assignment was to get the data from the papers that we read and manipulate it in order to be able to run it through the analysis software for next week. While processing our data we should also begin to see some correlation between the numbers and what our paper found as important.

2. I learned a few new tricks in Excel this week. I predict that during this next week I'll learn about many of the different pathways involved in heavy metal poisoning of *A. thaliana*

3. I was not able to finish all of the excel processing this week because I didn't know how to continue from processing all of the average log changes in regards to our specific data. I should have gone in to office hours last week to resolve this issue but I really didn't have time. I will resolve this issue as quickly as possible.

Michael R. Pina 01:53, 19 April 2010 (EDT)

## Janelle N. Ruiz

- The purpose of this assignment was to prepare our excel data file of our gene data to be run for analysis on GenMAPP.
- This week we were able to reformat variables in our data file and we learned the best way to format them to run in GenMAPP. We also learned that sometimes data is not always self-explanotory (we could not figure out how the authors calculated key variables in our excel file.
- I had questions but KP answered them.

## Bobak Seddighzadeh

- What is the purpose of this assignment? The purpose of this assignment was to familiarize us with our dataset, and more importantly to conduct some t-tests and other calculations that will aid us in the design of our experiment.
- What did you learn? Firstly, I learned how to use excel much better. I learned how to find averages and t-tests and the mechanical aspects of using excel.
- Do you have any questions still? Some of the sanity check steps were a little hard to follow. I was not sure what an avergae log FC test was.

- Electronic Journal

- Bobak Seddighzadeh Week 2
- Bobak Seddighzadeh Week 3
- Bobak Seddighzadeh Week 4
- Bobak Seddighzadeh Week 5
- Bobak Seddighzadeh Week 6
- Bobak Seddighzadeh Week 7
- Bobak Seddighzadeh Week 8
- Bobak Seddighzadeh Week 9
- Bobak Seddighzadeh Week 10
- Bobak Seddighzadeh Week 11
- Bobak Seddighzadeh Week 12
- Bobak Seddighzadeh Week 13

- Shared Journal

- BIOL398-01/S10:Class Journal Week 2
- BIOL398-01/S10:Class Journal Week 3
- BIOL398-01/S10:Class Journal Week 4
- BIOL398-01/S10:Class Journal Week 5
- BIOL398-01/S10:Class Journal Week 6
- BIOL398-01/S10:Class Journal Week 7
- BIOL398-01/S10:Class Journal Week 8
- BIOL398-01/S10:Class Journal Week 9
- BIOL398-01/S10:Class Journal Week 10
- BIOL398-01/S10:Class Journal Week 11
**BIOL398-01/S10:Class Journal Week 12**- BIOL398-01/S10:Class Journal Week 13

- Assignments

- BIOL398-01/S10:Week 2
- BIOL398-01/S10:Week 3
- BIOL398-01/S10:Week 4
- BIOL398-01/S10:Week 5
- BIOL398-01/S10:Week 6
- BIOL398-01/S10:Week 7
- BIOL398-01/S10:Week 8
- BIOL398-01/S10:Week 9
- BIOL398-01/S10:Week 10
- BIOL398-01/S10:Week 11
- BIOL398-01/S10:Week 12
- BIOL398-01/S10:Week 13

## Amanda Wavrin

- The purpose of this assignment was to begin our work with our Merrel et al.
*Vibrio cholerae*project. Completing this assignment allowed us to start working with our own DNA microarray data, the data that is specific to our paper on*V. cholerae*. Our dataset is now in GenMAPP version so we will be able to use them in lab this week. - While completing this assignment I got a much better understanding of how to analyze DNA microarray data while using excel. Not having a lot of background using excel, it was difficult to complete this assignment at first. After a little practice it became much easier.
- While following the instructions for this weeks assignment, I ran into some problems using excel. My computed p values did not match up with the expected results, leading me to beleive that I made a mistake along the way. I also had a difficult time creating and filling the "tstat" columns.

Amanda N. Wavrin 02:43, 19 April 2010 (EDT)

## Ryan Willhite

- What was the purpose of this assignment? The purpose of this assignment was to practice the analysis of DNA Microarray data in Xcel. It also gave us a chance to be proactive in inserting and organizing even more data that can be calculated using equations in excel to get average, standard deviation, etc.
- What did I learn from this assignment (head, hands, heart)? I learned how to input these equations to help organize as well as input more data to be analyzed. I also learned that simple changes in the equation can give false values which was a mistake pretty easy to make ; thank goodness for a partner.
- What did I not understand (yet) about this assignment? I still do not understand all of the reading of data and I do not understand why some values say "DIVO" and not able to derive some value, which caused some problems in averages, etc.

Ryan N. Willhite 11:43, 19 April 2010 (EDT)

## Kristoffer Chin

- The purpose of this assignment was to help us understand the data that we are working with with the DNA Microarray. It helps organize the data and understand the meaning of the numbers that are given to us in the XLS files. WE are also able to understand what the researched are actually looking at and which are significants
- I was able to practice my excel skills again. It helped me learn a little bit more on excel and the capabilities it has on data
- I am still having problem in reading the data in some ways. I am also having a problem on how I should be organizing the data so that it can be easily understandable. I need to find some kind of organization pattern that can easily be read.

--Kristoffer T. Chin 01:39, 19 April 2010 (EDT)