Purpose

Methods/Results/Electronic Notebook

1) Downloaded the gln3 data

2) Opened in Excel

3) Enabled Editing

4) Saved File with AS&CK_ before the rest of its name

5) Add a new sheet called ANOVA_dGLN3

6) Copied the Data from the Master_Sheet_dGLN3 to the new ANOVA_dGLN3

7) Created columns for Average Log called dGLN3_AvgLogFC_t for each time period adding 15,30,60,90, and 120 at the end.

8) Then we computed the average for the first row of t 15 time points of 2 through 5.

9) We copied down the formula all the rows

10)We noticed a DIV/0 Error for some rows since the data was blank.

11)Repeated the same process for the rest.

12)Creating a column for dGLN3_ss_HO for the sum of squares.

13) Highlighted the columns for all times for this and did =sumsq(all relevant data in the row)

14) Created Columns for dGLN3_ss_t15 through t120

15) Did the same process highlight the data in a row that applied to the specific time t.

16) Double clicked to expand

17) Was not the correct equation so deleted everything in the sumsq= that we just did except for the dGLN_ss_HO which was still correct

18) Instead we do number 14 in the worksheet.

19) For dGLN_ss_t15 the equation was =SUMSQ(D2:G2)-COUNTA(D2:G2)*X2^2

20) After completed copied down all the columns.

21) Created dGLN3_SS_full to the right.

22) Created the dGLN_Fstat to the

23) Took a weekend break

24) Back to the task

25) Added =SUM of the ss rows for the dGLN_SS_full

26) Double Clicked to Drop down for all of them

27) Counted my n for the fstat to be 20.

28) There was an error in my SS_Full, I should have only included the time times t15-120 and I accidentally included HO, removed it and the problem was fixed.

29) Now adding the Bonferroni and p value corrections

30) Created a box called dGLN3_Bonferroni_p-value and in the cell did = and selected AK2. Then did *6189.

31) Double clicked to fill the column.

32) Created a new column, dGLN3_Bonferroni_p-value correction. Entered =if(AL2>1,1,AL2) and then double clicked to expand down the formula.

33) Added a new worksheet to begin the Benjamini & Hochberg p value correction

34) Named worksheet dGLN3_ANOVA_B-H

35)Followed the Calculate the rest of the Benjamini & Hochberg p value correction section exactly.

36) Saved to upload to the wiki.

37) Uploaded to Wiki with same file name.

38) Continuing, now with the "Sanity Check".

39) Following the instruction and opening the dGLN3_ANOVA worksheet.

40) Did the Data Ribon > Filter. This is a shortcut to autofilter instead of using the top bars.

41) Expanded all the column headers so that they wouldn't be cut off by selecting all of them and double clicking between the column letter markers.

42) Clicked on the dropdown for the unadjusted p-value.

43) I selected a criterion to only show p-values less than to 0.05. There are 2531 genes with a p < 0.05.

44) I repeated the process of checking criterion but for 0.01, 0.001, and 0.0001. The results were:

1204 at 0.01, 514 at 0.001, 180 at 0.0001

45)Copying these into a new worksheet called data_checks.

46) Removed the filter on the dGLN_ANOVA worksheet. and verified the total entries are 6189.

47) Did the calculations for the % each number was out of 6189. These are the answers rounded. 40.90%, 19.45%, 8.31%, 2.91%

48) Did the same filtering for the Bonferroni and B&H p values for 0.05.

49) Added the answer to the data_checks sheet.

50) For some reason, my B&H had less results than the Bonferroni correction which makes me think there is somewhere that I did something wrong. For Bonferroni, I got 45 rows and for B&H I only have 10.

51) Now I am looking for NSR1. Searched for YGR159C and highlighted the row yellow and YGR159C and NSR1 boxes green. Its unadjusted P-value is 0.000506764. It's Bonferroni p-value is 3.136364678. It's B&H correct value is 1.

52) The average log fold change are as follows for YGR159C: t15 = 3.506225, t30 = 4.5319, t60 = 2.7592, t90 = -1.85025, t120 = -1.867425.

53) NSR1 does have a P-value of 0.0005 but that is unadjusted. It does not seem to change to cold shock when looking at the Bonferroni or B&H values.

54) Looking now at my favorite gene Sir2. YDL042C.

55) Located YDL042C and highlighted the row orange.

56) YDL042C's unadjusted P-value is 0.015418948. It's Bonferroni p-value is 95.42786686. It's B&H correct value is 1.

52) The average log fold change are as follows for YGR159C: t15 = 0.503525, t30 = 1.5781, t60 = 0.60005, t90 = -0.075175, t120 = -0.168375.

Data and Files

Media:AS&CK_BIOL367_S24_microarray-data_dGLN3.xlsx

Media:BIOL367_S24_Andrew_dGLN3_p-value_slide.pptx

Conclusion

--You will write a summary paragraph that gives the conclusions from this week's analysis.--

Acknowledgements & References

Acknowledgments, and References (as specified by the Week 1 assignment).

Acknowledgments

I worked on this assignment with Charlotte. I helped her with a lot of her excel stuff because I had more experience. I did not get help from her because I didn't need any in class. I texted her at 5:57 pm on wednesday about the p-values for B&H being strangely low for me.
You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
- I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
If you need to reference content (such as the methods of a protocol), that belongs in the References section where you will give a include a formal APA-formatted citation (see below).
You must also include this statement unless otherwise noted:
- "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
Sign your Acknowledgments section with your wiki signature.

References

In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
- methods
- data
- facts
- images
- documents, including the scientific literature
Do not include extraneous references that you do not cite or use on your page.
The references in this section should be accompanied by in text citations on your page that refer to these references.
The references should be formatted according to the APA guidelines.
For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.
Cite the appropriate weekly Assignment page. For example, the citation for the Week 1 Assignment page is:
- LMU BioDB 2024. (2024). Week 1. Retrieved January 8, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/Spring2024/index.php/Week_1
Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.