NicoleKalcic Week 8

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Journal Week 8 - Nicole Kalcic

Data Information

Strain Comparison: dHAP4

Individual dataset: File:BIOL367 Fall2017 Dahlquist-microarray-data-master 20171017NK.zip.xlsx

Powerpoint Slide:

File name:

Time points: t15, t30, and t60 have 4 and t90, t120 have 3


Electronic Journal

As noted above: we are comparing the dHAP4 data within the Yeast Gene Excel spreadsheet.

  1. Create a new worksheet, naming it "dHAP4_ANOVA".
  2. Copy the first three columns containing the "MasterIndex", "ID", and "Standard Name" from the "Master_Sheet" worksheet for your strain and paste it into your new worksheet. Copy the columns containing the data for your strain and paste it into your new worksheet.
  3. At the top of the first column to the right of your data, create five column headers of the form dHAP4_AvgLogFC_(TIME) where (TIME) is replaced with 15, 30, 60, 90, and then 120.
  4. In the cell below the dHAP4_AvgLogFC_t15 header, type =AVERAGE(D2:G2). Assuming steps 1-3 were done correctly, D2-G2 will indicate the data in row 2 associated with dHAP4 and t15. Complete this step by pressing the closing parenthesis (shift 0) the the "enter" key.
  5. This cell now contains the average of the log fold change data from the first gene at t=15 minutes.
  6. Click on this cell and position your cursor at the bottom right corner. You should see your cursor change to a thin black plus sign (not a chubby white one). When it does, double click, and the formula will magically be copied to the entire column of 6188 other genes.
  7. Repeat steps (4) through (8) with the t30, t60, t90, and the t120 data. Use step (7) on each corner. The other rows will look as follows:
    • For t30: =AVERAGE(H2:K2)
    • For t60: =AVERAGE(L2:O2)
    • For t90: =AVERAGE(P2:R2)
    • For t120: =AVERAGE(S2:U2)
  8. Now in the first empty column to the right of the dHAP4_AvgLogFC_t120 calculation, create the column header dHAP4_ss_HO.
  9. In the first cell below this header, type =SUMSQ(D2:U2). This will highlight all the LogFC data in row 2 for dHAP4 (avoiding the AvgLogFC rows). To complete this step, press the closing parenthesis (shift 0) and press the "enter" key.
  10. In the next empty column to the right of dHAP4_ss_HO, create the column headers dHAP4_ss_(TIME) as in (3).
  11. The headers will look as follows:
    • dHAP4_ss_t15
    • dHAP4_ss_t30
    • dHAP4_ss_t60
    • dHAP4_ss_t90
    • dHAP4_ss_t120
  12. To note: there are 3 data points for t90 and t120 (the rest have 4). Be careful when selecting these cells. The total number of data points is 18.
  13. In the first cell below the header dHAP4_ss_t15, type =SUMSQ(D2:G2)-COUNTA(D2:G2)*(V2)^2 and hit enter.
    • The COUNTA function counts the number of cells in the specified range that have data in them (i.e., does not count cells with missing values).
    • The phrase <D2:G2> is the data range associated with t15.
    • The phrase <V2> is the AvgLogFC for t15, and the "^2" squares that value.
    • Upon completion of this single computation, use the Step (7) trick to copy the formula throughout the column.
  14. Repeat this computation for the t30 through t120 data points. Again, be sure to get the data for each time point, type the right number of data points, and get the average from the appropriate cell for each time point, and copy the formula to the whole column for each computation.
  15. The other initial rows will look as follows, then you can complete step (7) on each corner
    • For t30: =SUMSQ(H2:K2)-COUNTA(H2:K2)*(W2)^2
    • For t60: =SUMSQ(L2:O2)-COUNTA(L2:O2)*(X2)^2
    • For t90: =SUMSQ(P2:R2)-COUNTA(P2:R2)*(Y2)^2
    • For t120: =SUMSQ(S2:U2)-COUNTA(S2:U2)*(Z2)^2
    • In the first column to the right of dHAP4_ss_t120, create the column header dHAP4_SS_full.
  16. In the first row below this header, type =SUM(AB2:AF2) and hit enter.


Summary Paragraph

Acknowledgements

I worked with my homework partner Blair Hamilton in class. We met face to face and then continued our communication through texting. She finished the assignment before me, and I used the set of her page Bhamilton18 Week 8 to guide an organization for mine.

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Nicolekalcic (talk) 18:46, 23 October 2017 (PDT)

References

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