User talk:Lenaolufson

Elena Olufson

---

Template:Lenaolufson

"100000" issue

• Lena, I've looked at the file. While I was looking, I uncovered an issue with how you made your "MasterSheet" worksheet. You were only supposed to copy over the columns that had the correct Cy5/Cy3 orientation. There should only be two technical replicates per sample in your MasterSheet.
• First fix your MasterSheet by getting rid of the columns you don't need.
• What we will do next is not delete the genes, but do a search and replace. You will search for "100000" and "-1000000" and replace it with an empty cell. In the find/replace window, type 100000 or -100000 in the find field and nothing at all in the replace field and then click on the replace all button and record the number of replacements.
• Then you can copy and paste special > paste values into your scaling and centering sheet and try again. You will know things are OK if your Average for each column is a very small number near zero and your standard deviation is near 1.

— Kdahlquist (talk) 16:38, 1 December 2015 (PST)

Week 12 Feedback

• I've looked at the compiled raw data that you posted and I have some feedback and next steps.
  1. Rename Sheet1 to "CompiledRawData".
  2. Rename your column heading as follows:
     • Call your leftmost column "ID" instead of Code.
     • For the data columns, you can get rid of the "(635/532)" from each header. While I understand what you are doing with the "A3-A5" nomenclature, it would be a little more clear if you called it something like "LogRatio_SampleA_Cy3-Cy5".
  3. Once you have renamed the columns, do all further manipulations in a different sheet. Copy and paste all of the data into Sheet2 which you should rename to "DyeSwap".
  4. 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 8448 (the number of spots on the microarray).
  5. Now, select all of the data and sort it A-->Z on the "ID" column.
  6. Delete all of the rows that have an ID of "_". Record the number of records left after you do that.
  7. Now you need to swap the dye orientation so that all of the samples are Cy5/Cy3.
     • Insert a column to the right of the columns that need to be swapped. Name the new column the same as you did before, but addd "_swapped" to the header to designate that you are going to swap the samples.
     • Then, type a formula in the column where you multiply the value that needs to be swapped by (-1). Copy and paste the formula to the entire column.
  8. Create a new worksheet that you name "MasterSheet". Copy and Paste special > Paste values the ID, MasterIndex, and data columns that are all in the orientation of Cy5/Cy3 (the original ones and the ones you just swapped).
  9. This is now your the starting point for the normalization and statistics. Copy and paste the data from this sheet into a new worksheet, which you should rename "ScalingCentering".
  10. In this new sheet, you should perform the scaling and centering according to the Vibrio cholerae instructions found here.]
  11. At this point, post your spreadsheet and e-mail Dr. Dahlquist and let me know where to find it. Your particular chip has duplicated spots on it, which we should average as another type of technical replicate. I have a script that will separate out the IDs so that you can easily average them in Excel. I will run the script and give you the results before you move on.
  12. Once this has been done, you will create a new sheet called "Statistics" and paste the values into this sheet.
      • You will then compute the average of the duplicate spots on the chip to get one value per chip.
      • You will then compute the average of the dye-swapped technical replicates to get one value per sample (A, B, C).
      • You will then compute the average of the averages for A, B, and C, to get the average of all samples.
      • You can then you should compute the T statistic, P value, Bonferroni adjusted p value, and Benjamini and Hochberg adjusted p value, according to the instructions you used for Vibrio cholerae.
  13. 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.
• Let me know if have questions.

— Kdahlquist (talk) 12:16, 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.
• Almost all requisite links to and from the user page as well as page categories are present, except:
  • The link from the individual journal entry back to your user page was missed.
• Electronic notebook was maintained.
• Work was submitted with corresponding summaries, but there were only 5 submissions. An assignment of this size can definitely be completed in smaller milestones; it is ideal to save your work after each of these milestones.

Database Exercises

Work in progress.

—Dondi (talk) 19:24, 25 October 2015 (PDT)

Week 4 Feedback

• Work was submitted mostly on time, with a small fix applied the next day.
• All good-habit items are largely fulfilled, with some suggestions for improvement:
  • All expected links and categories were noted, but the link from the journal entry to the user page is not part of the template. It will save you future trouble of you integrate this.
  • Electronic notebook content was seen.
  • Summaries were consistently provided for all edits, although there were only 5 of them. An assignment of this scale could certainly have been broken up into smaller pieces; this ensures that less work will be lost in the event of a power, software, or network failure.
• For the exercises, the following issues were seen; all others were correct:
  • You were off by one nucleotide on the transcription start site.
  • Because the transcription start site was off by one nucleotide, then the mRNA sequence was off by that single base as well.
• Shared responses were provided and they came in on time.

—Dondi (talk) 12:46, 7 October 2015 (PDT)

Week 3 Full Feedback

In addition to the early “good habit” notes previously given below, the following notes complete my response to your submissions:

• All of your command-line answers showed the correct results. Good job!
• One suggestion for presenting either code or plain data: if you begin a wiki line with an empty space, the text that follows it will be format in a “fixed width” format that fits code or plain data better. Give it a try and see how it looks to you.
• Regarding your shared journal entry, practice is definitely the way to get more comfortable with the command line. Allow yourself to make mistakes—with the commands that I have shown you so far, mistakes will be harmless and you can learn from them. There is definitely an unprecedented level of detail and precision involved when working with computers in this manner; but, as your chosen quote says, there is ultimately an art to it. Many arts require the same level of precision—you can think of coding precision as a very similar kind of exactitude.

—Dondi (talk) 16:52, 26 September 2015 (PDT)

Week 3 Early Feedback

My week 3 grading is not finished, but based on your week 2 feedback and what I have seen so far in Week 3, I thought I would chime in early so you can try to address these by the week 4 assignment.

• Good job in supplying a summary with all of your wiki contributions in Week 3! This is a good habit to maintain throughout the semester. You also accomplished this with a few more edits, which is also something to reinforce.
• Your Week 3 assignment still did not use the template that you’ve created; do make sure that you do so in Week 4 and beyond, because it contains all of the useful links that are checked for every assignment.
  • Please see Dr. Dahlquist’s instructions above for using the template in your journal pages.
  • Also make sure to add a link to your User Page within the template.
• Week 3 does not include the Journal Entry category either.
• Finally, a lab notebook aspect continues to be missing from your Week 3 submission. Your responses are almost entirely just the answers, with no notes on your thought process. As the computing assignments get harder, you will find this to be more and more crucial. Please give it a shot for Week 4.

That’s not everything yet, but I figured these were good points to make so that you can get a jump on them for Week 4.

—Dondi (talk) 09:18, 24 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; 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 7/14 contributions between the Week 1 and Week 2 deadlines. We are aiming to do this 100% of the time, so this needs a little work. Also, you completed the full assignment in only 3 edits to the wiki. You will want to consider saving your changes more frequently so that the granularity of the changes is smaller.
• For each week's assignment, you will need to create links from your User page to that week's assignment and to your individual and shared journal entries, as well as a link back from your individual journal entry and to the category "Journal Entry".
  • You have actually created all of these links on your template page (by borrowing the formatting from a fellow student, I see). However, what is missing is that you need to actually invoke the template on your user page and individual journal entry pages.
    • To do so, you need to use the syntax {{Lenaolufson}}, with the curly brackets, on your user page and on your Lenaolufson Week 2 page.
    • You could even invoke your template on all of your future individual journal assignment pages now, so you would never forget to do it again and would also avoid losing points for not providing the links.
• If you begin a line with a single space character, the text will appear in a fixed-width font, which is better for representing nucleic acid and protein sequences because they will then line up with each other better.
• With regards to your comments on your shared journal entry, you will see from the other students' comments, that others had issues with the Kaji and Kaji paper. It is sometimes the shortest papers that are the most difficult to understand!

— Kdahlquist (talk) 23:32, 18 September 2015 (PDT)

Week 1 Feedback

• I answered your question on my User talk page.
• The scores have not been posted yet, but I wanted to give you feedback on your Week 1 Assignment.
• Except for the email to Dr. Dahlquist and me, your assignment was submitted on time overall. Many of our assignments will be multipart like this one, so getting into a checklist habit will help you cover all the bases.
• Speaking of a checklist approach, your assignment is complete except for the items that I list below. I particularly like how you took advantage of external links in your work history and other areas of your page. You wrote something in the Summary field most of the time, although some were just generic indications of what sections got changed. See if you can get more descriptive as you get the hang of this; you’ll find that it makes your work more deliberate.
• Missing items:
  1. You did not indicate a snail mail address; withholding it on purpose is fine (say, for privacy reasons due to an off-campus address), but just as with the email to Dr. Dahlquist and me, we would have preferred an indication to that effect, to differentiate between forgetting to do it vs. not forgetting but preferring not to supply it.
  2. You defined headings down to just one level. Try to do multiple levels, at least 3 when appropriate, so that you can see how the headings give your page an outline structure.
  3. You created numbered lists as instructed, although in the Personal Interests section, with those single-item lists, a bulleted format would have been more appropriate. Even though you are checking off subtasks in this assignment, ideally you are also performing them in a context that matches their purpose well.
  4. Similarly, you did technically create and use a template, but said template does not really hold content that benefits from template automation. Ideally, your template contains something that will genuinely save you a lot of retyping in the future. The example that we mentioned in class was a template holding a quick-reference list for all of your pages—that will be very useful as a template because you will want to include that in every page you create, and will be a pain to retype every time. So, consider those practical elements when choosing to practice the basic wiki skills. That way it isn’t just a rote exercise and is actually something is useful for the rest of the semester.
• You will have the opportunity to make up some of the points you missed by completing the tasks listed above by the Week 2 deadline, midnight on September 15.

—Dondi (talk) 17:14, 9 September 2015 (PDT)

I have also answered your question on my user talk page. — Kdahlquist (talk) 23:18, 10 September 2015 (PDT)