User talk:Helena M. Olivieri

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(feedback on week 9 spreadsheet)
Current revision (15:57, 19 April 2013) (view source)
(Further Feedback Week 12 Individual Journal: discrepancy between profile and go and TF results)
 
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== Week 12 Journal Feedback ==
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* Thank you for submitting your assignment on time.
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* I was unable to check your work with regard to the GO terms and YEASTRACT because you did not post your GO list file and Gene list file on LionShare.  Please post the files for profile 45 and send me the link.
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* Profile 45 is a profile of genes whose expression is up-regulated at the cold shock time points and then down-regulated at the recovery time points.  ''All'' the genes in that profile fit that pattern.  Since the GO terms are associated with the genes in that profile, then you can think of them as similarly up-regulated during cold shock and down-regulated during recovery.  In other words, each of the GO terms that are associated with that profile contains genes that are up-regulated during cold shock and then down-regulated during recovery.
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* Remember that each individual journal page needs to link back to your User page, link to the original assignment page, and needs to have the category BIOL398-03/S13.
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=== Week 12 Shared Journal Feedback ===
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* For question 4 of the shared journal reflection, be careful in the way you state your answer. The individual gene's p value just tells us that we would see that big of a change in gene expression due to chance, that percentage of the time.  The profile and GO term p values do not refer to individual genes. The profile p value is a measure of the probability that you would see that many genes that fit that expression profile due to chance. The GO term p value is a measure of the probability that you would see that many genes in that profile associated with that GO term due to chance. The latter two p values are dealing with groups of genes, not individual genes.  Also, the Gene Ontology terms and transcription factors are two separate considerations.  GO terms are associated with a group of genes who all play a part in that process the term describes.  There ''are'' some terms related to transcription and transcription factors, but most GO terms are related to other parts of a cell's physiology.  YEASTRACT tells us about which transcription factors regulate a group of genes.
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''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 15:30, 19 April 2013 (EDT)''
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=== Further Feedback Week 12 Individual Journal ===
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* I received your files.  I looked at the GO list file for profile 45 and it has 164 GO terms (not 165) that are p < 0.05; it has 104 GO terms (not 35) that have a corrected p < 0.05.
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* The GO terms that you list the definitions for do not seem to be the top terms for profile 45, which profile did you use?
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* Also, the top transcription factors do not seem to be from profile 45 either, which profile did you use?
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''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 15:55, 19 April 2013 (EDT)''
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== Week 9 Spreadsheet Feedback ==
== Week 9 Spreadsheet Feedback ==

Current revision

Contents

Week 12 Journal Feedback

  • Thank you for submitting your assignment on time.
  • I was unable to check your work with regard to the GO terms and YEASTRACT because you did not post your GO list file and Gene list file on LionShare. Please post the files for profile 45 and send me the link.
  • Profile 45 is a profile of genes whose expression is up-regulated at the cold shock time points and then down-regulated at the recovery time points. All the genes in that profile fit that pattern. Since the GO terms are associated with the genes in that profile, then you can think of them as similarly up-regulated during cold shock and down-regulated during recovery. In other words, each of the GO terms that are associated with that profile contains genes that are up-regulated during cold shock and then down-regulated during recovery.
  • Remember that each individual journal page needs to link back to your User page, link to the original assignment page, and needs to have the category BIOL398-03/S13.

Week 12 Shared Journal Feedback

  • For question 4 of the shared journal reflection, be careful in the way you state your answer. The individual gene's p value just tells us that we would see that big of a change in gene expression due to chance, that percentage of the time. The profile and GO term p values do not refer to individual genes. The profile p value is a measure of the probability that you would see that many genes that fit that expression profile due to chance. The GO term p value is a measure of the probability that you would see that many genes in that profile associated with that GO term due to chance. The latter two p values are dealing with groups of genes, not individual genes. Also, the Gene Ontology terms and transcription factors are two separate considerations. GO terms are associated with a group of genes who all play a part in that process the term describes. There are some terms related to transcription and transcription factors, but most GO terms are related to other parts of a cell's physiology. YEASTRACT tells us about which transcription factors regulate a group of genes.

Kam D. Dahlquist 15:30, 19 April 2013 (EDT)

Further Feedback Week 12 Individual Journal

  • I received your files. I looked at the GO list file for profile 45 and it has 164 GO terms (not 165) that are p < 0.05; it has 104 GO terms (not 35) that have a corrected p < 0.05.
  • The GO terms that you list the definitions for do not seem to be the top terms for profile 45, which profile did you use?
  • Also, the top transcription factors do not seem to be from profile 45 either, which profile did you use?

Kam D. Dahlquist 15:55, 19 April 2013 (EDT)

Week 9 Spreadsheet Feedback

  • I have reviewed the spreadsheet you have submitted for the Week 9 assignment. Unfortunately, you made a typo on your "scaled_centered" worksheet that has affected all of your downstream calculations. In the STDEV calculation, your the range of cells in your formula went to row 9192 instead of 6192. You will need to correct this before going on to the Week 12 assignment.

Kam D. Dahlquist 01:38, 9 April 2013 (EDT)

Week 1 Journal Feedback

  • Thank you for submitting your assignment on time.
  • There are a few of things that you need to fix on your individual user page and shared journal page. Please make these changes by next week's journal deadline (midnight, February 8) to earn back the points you missed on this assignment.
    1. You need to put the complete street address for your box at LMU.
    2. Please let us know on your user page or via e-mail if you have any worries/concerns about the class and if there is anything else you want us to know, even if the answer is "no".
    3. On the Week 1 shared journal page, make a link back to your user page at the top of the section where you answered the questions.
    4. You are not using summary field when you make changes to the wiki. The goal is to fill it out every time you make a change.
    5. Your template is missing. Please create one and invoke it from your user page and all of your individual journal pages. It should contain links for each of the class assignment pages, your journal pages, and the class shared journal pages. It is also helpful to put the class category on it as well. Currently, the link to the shared journal assignment and the category is currently missing from your user page. If you put it in your template and then invoke the template, you will never forget to put it in your journal page.
  • Please feel free to delete the welcome message from OpenWetWare below.

Kam D. Dahlquist 19:13, 30 January 2013 (EST)


Helena, I answered your question on my user talk page. Kam D. Dahlquist 20:04, 24 January 2013 (EST)


You asked: "Hi Dr. Fitzpatrick, What are some of your hobbies outside of academia? Helena M. Olivieri 01:12, 23 January 2013 (EST)"

My answer: I have quite a few. I like to travel, when I can afford it and make time for it. I (attempt to) play guitar. I do some woodworking, and I like to take pictures.

Ben G. Fitzpatrick 14:02, 3 February 2013 (EST)


Week 2 Journal Feedback

  • For future assignments, please plan ahead and submit your work on time.
  • Your discussion is a bit thin. You need to include a little more detail on the simulations you performed.
  • Graphs would be very helpful in backing up your discussion. See Elizabeth's page for a good example of a file containing some well-annotated simulations, or Ashley's for graphs embedded in the discussion. Paul's screencaps, while a bit difficult to view due to size, may also help you.
  • How might you model the ethanol production as a third differential equation? How might it impact the mortality?

Ben G. Fitzpatrick 13:52, 4 February 2013 (EST)

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