User talk:Kzebrows
From LMU BioDB 2015
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Week 12 Feedback
- The OTC Files page needs to have your team's template on it.
- I've looked at the compiled raw data that you and Erich posted and I have some feedback and next steps. I'm putting the instructions here, but you should share them with Erich. I'll put a note on his talk page to look here as well.
- First, I'm not sure that I understand the question you posed in your e-mail. Your dataset has 4 treatments (0.5X RX, 1X RX, 0.5X RP, 1X RP), with 3 timepoints each (10, 30, and 60 minutes), with 3 biological replicates each. Thus there are 9 samples per treatment for a total of 36 chips, which you have accounted for in your compiled raw data. Each of these treatment samples was competitively hybridized against a control sample that was just treated with methanol (which is what the antibiotics were dissolved in). As you determined in class last week, there are no dye swaps in your data; the drug-treated sample was always labeled with Cy5 and the control was always treated with Cy3.
- Generally, I like how you have named your column headers. However, I would like you to spell out "LR" as either "LogRatio" or LogFC, to be more explicit as to what that is. You should double-check that all your punctuation is consistent from sample to sample (blank spaces, hyphens, etc.).
- In you compiled raw data file, leave your Sheet1 (rename it to CompiledRawData) as is and do all further manipulations in a different sheet. Copy and paste all of the data into Sheet2 which you should rename to "MasterSheet".
- You can go ahead and delete all of the extra "ID" columns that you copied from each individual data file, just leaving one ID column as the left-most column (Column A). Rename that Column as "ID".
- Create a "MasterIndex" column as follows. Insert a new column to the right of the "ID" column and name it "MasterIndex". In this column you will create a numerical index of genes so that you can always sort them back into the same order that they started out in.
- Type a "1" in cell B2 and a "2" in cell B3.
- Select both cells. Hover your mouse over the bottom-right corner of the selection until it makes a thin black + sign. Double-click on the + sign to fill the entire column with a series of numbers from 1 to 4224 (the number of spots on the microarray).
- Now, select all of the data and sort it A-->Z on the "ID" column.
- Delete all of the rows that have an ID of "Empty" or "Blank###". Record the number of records left after you do that.
- Sort it back by the "MasterIndex" column to put the IDs back in the order that they started in (except that some will now be missing).
- Do a Find and Replace where you find all of the cells that contain the word "Error" and replace it with nothing. Record the number of cells that are replaced that way.
- This is now your the starting point for the normalization and statistics. Copy and paste the data from this sheet into Sheet3, which you should rename "ScalingCentering".
- In this new sheet, you should perform the scaling and centering according to the Vibrio cholerae instructions found here.]
- Once you have done the scaling and centering, you can create a new sheet called "Statistics" and paste the values into this sheet. You should then compute the Average for each treatment and timepoint (there will be 12 different averages), then you should compute the T statistic, P value, Bonferroni adjusted p value, and Benjamini and Hochberg adjusted p value for each of the treatments and timepoints. It seems that a divide and conquer approach like you already adopted will be good; you do the statistics for one drug and Erich does the other.
- After that, then you will need to then format it for GenMAPP and you'll be ready to import it into GenMAPP and run MAPPFinder.
- When you have done the scaling and centering, will you post that file and e-mail me so I can look at it? You can still move forward with the other steps, but I just want to see the results of that particular manipulation.
- If you have any questions, please let me know. — Kdahlquist (talk) 11:25, 24 November 2015 (PST)
Week 6 Feedback
I’ve chosen to issue partial feedback sooner than complete feedback later, in case it will help you address issues with Week 8.
Best Practices
- Individual and shared work were both submitted on time.
- Requisite links to and from the user page as well as page categories are all present.
- Electronic notebook was maintained.
- Work was submitted in appropriate frequencies with corresponding summaries.
- This amounts to a “best practices” perfect score. Good work, keep it up!
Database Exercises
Work in progress.
—Dondi (talk) 16:45, 25 October 2015 (PDT)
Week 4 Feedback
- Work was submitted on time, with 5 minutes to spare.
- All good-habit items are fulfilled:
- All expected links and categories were noted.
- Electronic notebook content was seen.
- Summaries were consistently provided over a good number of edits.
- For the exercises, the following issues were seen; all others were correct:
- You were off by one nucleotide on the transcription start site.
- The incorrect stop codon was chosen.
- There is an inconsistency between the mRNA electronic notebook and the final command—the change from t to u is mentioned in the notebook but not seen in the command itself.
- The incorrect stop codon means that the amino acid sequence ended at the wrong place as well; further, a spacing glitch in the commands kept the codons from being “tripled out” correctly.
- Shared responses were provided and they came in on time.
—Dondi (talk) 23:29, 4 October 2015 (PDT)
Week 3 Feedback
- Work was submitted on time, though with just around a half-hour to spare. See if you can give yourself additional wiggle room in case you experience unexpected delays.
- All good-habit items are largely fulfilled:
- All expected links and categories were noted.
- You phased your work well and you consistently supplied a change summary with all but one of your wiki edits.
- You accompanied your work with electronic notes and processes for the reading frames section, but the details thinned out noticeably when it got to the xmlpipedb-match questions.
- All exercises were performed or answered correctly:
- There is a small typo in your complement answer—the period at the end of the command sequence is extraneous and will actually generate an error if the commands are copy-pasted exactly (amazing what trouble a single dot can cause).
- In your commentary, “caret” was misspelled as “carrot.” They sound the same, but don’t look the same :)
- Thank you for your candor in your shared responses. Yes, we are definitely outside biologists’ comfort zones now; hang in there and it’s good to hear that you find this foray rewarding. Definitely practice is valuable here, so keep at it and don’t hesitate to ask if you get stuck.
—Dondi (talk) 19:12, 26 September 2015 (PDT)
Week 2 Feedback
- Although, the Week 2 scores have not yet been posted, I want to give you feedback on the assignment that you can incorporate to your your Week 3 submission.
- First, thank you for submitting your assignment on time.
- Your translations are correct, except for frame +3, which contains a missense mutation (another motivation for doing this by computer such as in the Week 3 assignment); although it would have been better for completeness to go ahead and translate the rest of the sequence after the stop codon, in this case.
- You did not include anything by the way of an electronic notebook for this assignment. Although this assignment was pretty straightforward, you still need to document the process of what you did to arrive at the answers, not just supply the answers. Please be sure to do this for your Week 3 submission.
- You wrote something in the Summary field for 11/11 contributions between the Week 1 and Week 2 deadlines, keep up the good work! However, you completed the full assignment in only 2 edits to the wiki. This suggests that you are doing the work outside the wiki and then pasting it in. Ideally, you should do the work natively in the wiki environment. Even if this is not the case, you will want to consider saving your changes more frequently so that the granularity of the changes is smaller.
- You have set up your template and completed all the links requested.
- The relationship between sense and antisense strands that you mention in your wiki does not always hold. In a real gene, only one frame will be an open reading frame and all other frames will contain a stop codon, actually.
- With regards to your comments on your shared journal entry, I knew that the Nirenberg article would be difficult for folks without a biology background and even with a biology background. However, I also think it's a good exercise to go back to the original source sometimes and read about discoveries from "the horse's mouth" so to speak.
— Kdahlquist (talk) 23:11, 20 September 2015 (PDT)
Week 1 Feedback
- I answered your question on my user talk page.
- I am going to provide feedback on your Week 1 Assignment, even thought he scores are not yet posted.
- Thank you for submitting your assignment on time.
- Your assignment is neat and complete, but the following items need work:
- You wrote something in the Summary field for 17 out of 22 contributions, or about 77% of the time. You should aim to write something there 100% of the time. Don't forget to do that when you upload files as well.
- You did create links within the wiki. However, you formatted them like external links instead of internal links. For example, you can successfully link to the Main page of this wiki by formatting it like an external link like this: [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Main_Page Main page], but it is better to use the internal link syntax: [[Main Page | Main Page]]. Please convert all of your internal wiki links to the internal syntax.
- Your external links to Eugene and TriDelta are broken because you have extraneous information in your URLs. The format of a URL begins with http:// or https:// followed by either www.domain.extension or just domain.extension where the common extensions are .com, .org, or .edu. If you are copying and pasting a link from your browser address field, don't type an extra http://. Let us know if you have questions about this.
- You uploaded and linked to a file, but it has a very generic filename. It would be better to include your name and the date in your filename so there is not any confusion with other people's files.
- Please delete the category "User Page" that you additionally created.
- You will have the opportunity to make up the points that you missed by making the above corrections by the Week 2 journal deadline.
— Kdahlquist (talk) 23:09, 9 September 2015 (PDT)
I’ve answered your question on my talk page.
