# Difference between revisions of "User talk:Salman Ahmad"

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+ | == Week 12 Feedback == | ||

+ | |||

+ | * Thank you for submitting your assignment on time. | ||

+ | * You included screenshots from your STEM results of profiles that were not significant. Only the profiles that showed up in color in the first results screen were significant and should be considered. | ||

+ | * You did not explicitly state which profile you chose, although it appears to be #23. | ||

+ | * In answer to the question how many GO terms had a p value of < 0.05, you said 533, but it is really 116. In answer to how many GO terms had a corrected p value of 0.05, you answered 116, but it is really 44. | ||

+ | * The RegulationMatrix file that you uploaded had the wrong file extension, ".ppt" instead of ".xls". | ||

+ | * In your narrative, you mention that you only want to add the transcription factors RAP1 and STE12, but in your file, SOK2, MSN2, and YAP5 are there as well. Did you mean to add them? | ||

+ | * In your discussion of the interpretation of the GO terms, you need to be specific about why the cell is up-/down-regulating these specific GO terms in response to cold. | ||

+ | * Remember, you need to link back to the original assignment page from every individual journal page. | ||

+ | |||

+ | ''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 13:01, 18 April 2013 (EDT)'' | ||

+ | |||

+ | === Week 12 Shared Journal Feedback === | ||

+ | |||

+ | * The STEM profiles were listed in order of significance. The ones with the ''lowest'' p value were listed first. The profiles that showed up in color were all significant, and the white ones were not. The p value depends on the ratio of the number of genes in the profile versus the number of genes that would be expected in that profile due to chance. | ||

+ | * For question 4 of the shared journal reflection, be careful in the way you state your answer. 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. | ||

+ | |||

+ | ''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 13:36, 18 April 2013 (EDT)'' | ||

+ | |||

+ | == Week 9 Spreadsheet Feedback == | ||

+ | |||

+ | * I've reviewed the spreadsheet you submitted for your week 9 assignment. It all looks correct, except for the following: | ||

+ | ** On the "statistics" worksheet, you made a mistake on the formula for the Average Log Fold Change for t15. The cell reference in the formula does not include all of the replicates for t15. This will need to be fixed before doing the Week 12 assignment. | ||

+ | ** In formatting your "final" worksheet, you had four decimal places for the fold changes, not the two decimal places requested in the protocol. | ||

+ | |||

+ | ''— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 01:35, 9 April 2013 (EDT)'' | ||

+ | |||

== Week 1 Journal Feedback == | == Week 1 Journal Feedback == | ||

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— [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 02:20, 31 January 2013 (EST) | — [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 02:20, 31 January 2013 (EST) | ||

---- | ---- | ||

− | Hello, Salman Ahmad | + | You asked: "Hello Dr. Fitzpatrick: Students are learning higher levels of math earlier in their lives than before, how do you think that will affect the applications of math in the future? Salman Ahmad 21:23, 22 January 2013 (EST)" |

+ | |||

+ | My answer: That's a really good question. I don't think universities in general (or LMU in particular) have caught up educational programs to the way students are being taught pre-college. College calculus classes (depending on the professor) can be very different from high school ones, tho. I'd hope that it will help "across the board" with people being able to approach a lot of things more quantitatively. So many applications today involve large data sets in which the data points have many attributes (we often call this high dimensional data). I think the need may drive the math, rather than the other way around. We may see the type of math taught changing from calculus based stuff to linear algebra (vectors and matrices), statistical, and computational. | ||

− | + | '''[[User:Ben G. Fitzpatrick|Ben G. Fitzpatrick]] 14:00, 3 February 2013 (EST)''' | |

− | |||

− | |||

− | |||

− | |||

− | |||

− | |||

− | + | == Week 2 Journal Feedback == | |

− | + | * Thanks for submitting 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 waste with the differential equations? | ||

− | + | '''[[User:Ben G. Fitzpatrick|Ben G. Fitzpatrick]] 14:00, 4 February 2013 (EST)''' | |

+ | |||

+ | ---- |

## Latest revision as of 09:36, 18 April 2013

## Contents

## Week 12 Feedback

- Thank you for submitting your assignment on time.
- You included screenshots from your STEM results of profiles that were not significant. Only the profiles that showed up in color in the first results screen were significant and should be considered.
- You did not explicitly state which profile you chose, although it appears to be #23.
- In answer to the question how many GO terms had a p value of < 0.05, you said 533, but it is really 116. In answer to how many GO terms had a corrected p value of 0.05, you answered 116, but it is really 44.
- The RegulationMatrix file that you uploaded had the wrong file extension, ".ppt" instead of ".xls".
- In your narrative, you mention that you only want to add the transcription factors RAP1 and STE12, but in your file, SOK2, MSN2, and YAP5 are there as well. Did you mean to add them?
- In your discussion of the interpretation of the GO terms, you need to be specific about why the cell is up-/down-regulating these specific GO terms in response to cold.
- Remember, you need to link back to the original assignment page from every individual journal page.

*— Kam D. Dahlquist 13:01, 18 April 2013 (EDT)*

- The STEM profiles were listed in order of significance. The ones with the
*lowest*p value were listed first. The profiles that showed up in color were all significant, and the white ones were not. The p value depends on the ratio of the number of genes in the profile versus the number of genes that would be expected in that profile due to chance. - For question 4 of the shared journal reflection, be careful in the way you state your answer. 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.

*— Kam D. Dahlquist 13:36, 18 April 2013 (EDT)*

## Week 9 Spreadsheet Feedback

- I've reviewed the spreadsheet you submitted for your week 9 assignment. It all looks correct, except for the following:
- On the "statistics" worksheet, you made a mistake on the formula for the Average Log Fold Change for t15. The cell reference in the formula does not include all of the replicates for t15. This will need to be fixed before doing the Week 12 assignment.
- In formatting your "final" worksheet, you had four decimal places for the fold changes, not the two decimal places requested in the protocol.

*— Kam D. Dahlquist 01:35, 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.
- You need to put the complete street address for your box at LMU.
- On the Week 1 shared journal page, put the link to your user page underneath the header for your section.
- In addition to posting a question on Dr. Fitzpatrick's talk page, you need to post a question on my talk page.
- You have not filled out the summary field when you save changes to your pages. You need to fill it out
*every time*you make a change. - You need to demonstrate that you can "comment out" something. Your comment was just what was put there by the OpenWetWare script.
- Your link to a file needs a label. What you did works, but it would be better to use the complete wiki syntax. I.e., use [[Media:AhmadResume.doc | my resume]], which looks like this: my resume, instead of just Media:AhmadResume.doc.
- While you have created a template, you have not actually
*invoked*it on your page. To invoke your template, use the wiki syntax {{Salman Ahmad}} on your page. Furthermore, you need to use your template to your advantage. 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 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 message from OpenWetWare below.

— Kam D. Dahlquist 02:20, 31 January 2013 (EST)

You asked: "Hello Dr. Fitzpatrick: Students are learning higher levels of math earlier in their lives than before, how do you think that will affect the applications of math in the future? Salman Ahmad 21:23, 22 January 2013 (EST)"

My answer: That's a really good question. I don't think universities in general (or LMU in particular) have caught up educational programs to the way students are being taught pre-college. College calculus classes (depending on the professor) can be very different from high school ones, tho. I'd hope that it will help "across the board" with people being able to approach a lot of things more quantitatively. So many applications today involve large data sets in which the data points have many attributes (we often call this high dimensional data). I think the need may drive the math, rather than the other way around. We may see the type of math taught changing from calculus based stuff to linear algebra (vectors and matrices), statistical, and computational.

**Ben G. Fitzpatrick 14:00, 3 February 2013 (EST)**

## Week 2 Journal Feedback

- Thanks for submitting 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 waste with the differential equations?

**Ben G. Fitzpatrick 14:00, 4 February 2013 (EST)**