Knguye66 Eyoung20 Week 12/13

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Combined Individual Journals for Kaitlyn Nguyen and Emma Young (Data Analysts).

Purpose

The purpose of this assignment is to record our progress towards the FunGals group deliverables as the Data Analysts for this week and the future weeks to come.

Methods and Results: Progress

Progress 11/21/19

  • Our group decided to have the ANOVA, sanity check, and STEM set-up done before class on Thursday, 11/21/19
  • First created a worksheet and labeled accordingly based on the format the Coder's Guild decided
  • Finished the steps on Week 8 for Statistical Analysis Part I: ANOVA on Microsoft Excel for the new MicroArray Data found on the Data Analysis page
    • For questions asked on the p-value (use: "out of 4468" genes instead of "out of 6189" to adjust for this data)
  • Following the ANOVA: Part I, Bonferroni, Benjamini & Hochberg, and p-value correction, a quick sanity check was performed for the p-value dataset.

Sanity Check Questions:

-Unadjusted p-value-

  1. How many genes have p<0.05? and what is the percentage (out of 4468)?
    • 1196
  2. How many genes have p<0.01? and what is the percentage (out of 4468)?
    • 731
  3. How any genes have p<0.001? and what is the percentage (out of 4468)?
    • 380
  4. How many genes have p<0.0001? and what is the percentage (out of 4468)?
    • 190

-Bonferroni & Benjamini and Hochberg p-value-

  1. How many genes are p<0.05 for the Bonferroni-corrected p-value? and what is the percentage (out of 4468)?
    • 103, 2.3%
  2. How many genes are p <0.05 for the Benjamini and Hochberg-corrected p-value? and what is the percentage (out of 4468)?
    • 677, 15.2%
  1. Prepare your microarray data file for loading into STEM.
    • Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
    • Select all of the data from your "(STRAIN)_ANOVA" worksheet and Paste special > paste values into your "(STRAIN)_stem" worksheet.
      • Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
      • Filter the data on the B-H corrected p value to be > 0.05 (that's greater than in this case).
        • Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise.
      • Delete all of the data columns EXCEPT for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
      • Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
      • Save your work. Then use Save As to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
        • Note that you should turn on the file extensions if you have not already done so.
  2. Now download and extract the STEM software. Click here to go to the STEM web site.

Conclusion

The first stage of our group's project was completed via referencing Week 8 and using Microsoft Excel to complete the tasks. The excel file will be located in the FunGals page for viewing and download.

Acknowledgements

This section is in acknowledgement to partner Kaitlyn Nguyen (User:knguye66), Michael Armas (User:Marmas), as well as, Iliana Crespin (User:Icrespin), and Emma Young (User:eyoung20). We would also like to acknowledge Dr. Dahlquist (User:KDahlquist) for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source." Knguye66 (talk) 18:49, 20 November 2019 (PST)

References

User Page

User:knguye66

Template Page

Template:knguye66


Table of all assignments and journal entries for BIO-367-01

Week Individual Journal Entry Shared Journal
Week 1 - Class Journal Week 1
Week 2 knguye66 Week 2 Class Journal Week 2
Week 3 ILT1/YDR090C Week 3 Class Journal Week 3
Week 4 knguye66 Week 4 Class Journal Week 4
Week 5 DrugCentral Week 5 Class Journal Week 5
Week 6 knguye66 Week 6 Class Journal Week 6
Week 7 knguye66 Week 7 Class Journal Week 7
Week 8 knguye66 Week 8 Class Journal Week 8
Week 9 knguye66 Week 9 Class Journal Week 9
Week 10 knguye66 Week 10 Class Journal Week 10
Week 11 knguye66 Week 11 FunGals
Week 12/13 knguye66 Eyoung20 Week 12/13 FunGals
Week 15 knguye66 Eyoung20 Week 15 Class Journal Week 15

Eyoung20 user page

Assignment pages Individual Journal Class Journal
week 1 Eyoung20 journal week 1 Class Journal Week 1
week 2 Eyoung20 journal week 2 Class Journal Week 2
week 3 ASP1/YDR321W Week 3 Class Journal Week 3
week 4 Eyoung20 journal week 4 Class Journal Week 4
week 5 Ancient mtDNA Week 5 Class Journal Week 5
week 6 Eyoung20 journal week 6 Class Journal Week 6
week 7 Eyoung20 journal week 7 Class Journal Week 7
week 8 Eyoung20 journal week 8 Class Journal Week 8
week 9 Eyoung20 journal week 9 Class Journal Week 9
week 10 Eyoung20 journal week 10 Class Journal Week 10
week 11 Eyoung20 journal week 11 FunGals
week 12/13 Knguye66 Eyoung20 Week 12/13 FunGals
week 15 Knguye66 Eyoung20 Week 15 FunGals
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